Methods, systems, and kits for evaluating multiple sclerosis

ABSTRACT

The present invention provides a method for evaluating multiple sclerosis (MS), or excluding MS as a diagnosis for a patient The method comprises determining a gene expression profile for a sample from such a patient. The gene expression profile, which contains gene expression values for a plurality of genes that are differentially expressed in white blood cells of MS patients, is compared to an MS-profile and/or a non-MS profile, and classified. The invention also provides a method for monitoring treatment of an MS patient Pre-treatment and post-treatment gene expression profiles contain gene expression values for a plurality of genes that are differentially expressed upon treatment of MS patients. The expression profiles may then be compared, to identify differences between pre-treatment and post-treatment gene expression. These differences are indicative of the patient&#39;s response to treatment The invention further provides kits and systems for performing the methods of the invention.

PRIORITY

This application claims priority to U.S. Provisional Application No. 60/924,671 filed May 25, 2007, which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to methods, systems, and kits for evaluating multiple sclerosis (MS), and for assisting in the diagnosis, prognosis, and/or treatment of MS.

SEQUENCE LISTING

The contents of the accompanying Sequence Listing are hereby incorporated by reference.

BACKGROUND OF THE INVENTION

Multiple sclerosis (MS) is a disease that affects the central nervous system, and can range from relatively benign to somewhat disabling to devastating. In MS, the myelin surrounding nerve cells is damaged or destroyed, impacting the ability of the nerves to conduct electrical impulses to and from the brain, and leaving scar tissue called sclerosis. These damaged areas are also known as “plaques” or “lesions.” According to the National Multiple Sclerosis Society, there are approximately 400,000 individuals with MS in the United States.

The first symptoms of MS typically appear between the ages of 20 and 40, and include blurred or double vision, red-green color distortion, or even blindness in one eye. Most MS patients experience muscle weakness in their extremities and difficulty with coordination and balance. In severe cases, MS can produce partial or complete paralysis. Paresthesias (numbness, prickling, or “pins and needles”), speech impediments, tremors, and dizziness are frequent symptoms of MS. Approximately half of MS patients experience cognitive impairments.

Diagnosing MS is complicated, because there is no single test that can confirm the presence of MS. The process of diagnosing MS typically involves criteria from the patient's history, a clinical examination, and one or more laboratory tests, with all three often being necessary to rule out other possible causes for symptoms and/or to gather facts sufficient for a diagnosis of MS.

Magnetic resonance imaging (MRI) is a preferred test. An MRI can detect plaques or scarring possibly caused by MS. However, an abnormal MRI does not necessarily indicate MS, as lesions in the brain may be associated with other disorders. Further, spots may also be found in healthy individuals, particularly in healthy older persons. These spots are called UBOs, for unidentified bright objects, and are not related to an ongoing disease process. In addition, a normal MRI does not absolutely rule out the presence MS. About 5% of individuals who are confirmed to have MS on the basis of other criteria, have no brain lesions detectable by MRI. These individuals may have lesions in the spinal cord or may have lesions that cannot be detected by MRI.

A diagnosis of MS might be made based on an evaluation of symptoms, signs, and the results of an MRI, but additional tests may be ordered as well. These include tests of evoked potential, cerebrospinal fluid, and blood.

For example, cerebrospinal fluid is sampled by a lumbar puncture, and is tested for levels of immune system proteins and for the presence of an antibody staining pattern called “oligoclonal bands.” Oligoclonal bands indicate an immune response within the central nervous system and are found in the spinal fluid of 90-95% of individuals with MS. However, oligoclonal bands are also associated with diseases other than MS, and therefore the presence of oligoclonal bands alone is not definitive of MS.

There is likewise no definitive blood test for MS, but blood tests can exclude other possible causes for various neurologic symptoms, such as Lyme disease, collagen-vascular diseases, rare hereditary disorders, and AIDS.

Diagnosing MS generally requires: (1) objective evidence of at least two areas of myelin loss, or demyelinating lesions, “separated in time and space” (lesions occurring in different places within the brain, spinal cord, or optic nerve-at different points in time); and (2) all other diseases that can cause similar neurologic symptoms have been objectively excluded. Until (1) and (2) have been satisfied, a physician does not make a definite diagnosis of MS.

Depending on the clinical problems present when an individual sees a physician, one or more of the tests described above might be performed. Sometimes tests are performed several times over a period of months to help gather the necessary information. A definite MS diagnosis must satisfy the McDonald criteria, named for the distinguished neurologist W. Ian McDonald who sparked society-supported efforts to make the diagnostic process for MS faster and more precise.

There are a few distinct clinical courses for MS, referred to as relapsing-remitting MS, secondary-progressive MS, progressive-relapsing MS, and primary progressive MS. Relapsing-remitting MS is characterized by clearly-defined, acute attacks (relapses), usually with full or partial recovery, and no disease progression between attacks. Secondary-progressive MS is initially relapsing-remitting but then becomes continuously progressive at a variable rate, with or without occasional relapses along the way. The disease-modifying medications are thought to provide benefit for those who continue to have relapses. Primary progressive MS may be characterized by disease progression from the beginning with few or no periods of remission. Progressive-relapsing MS is characterized by disease progression from the beginning, but with clear, acute relapses along the way.

There are several options available for treating individuals diagnosed with MS. Beta-interferon (Avonex, Betaseron, Rebif) has been approved to treat MS. Interferons are also made by the body, mainly to combat viral infections. Interferons have been shown to decrease the worsening or relapse of MS, however disease progression remains unaffected and the side effects of interferons are poorly tolerated. Glatiramer acetate (Copaxone) is a mixture of amino acids that has been shown to decrease the relapse rates of MS by 30%, and appears to also have a positive effect on the overall level of disability. Glatiramer acetate is better tolerated than the interferons and has fewer side effects. Glatiramer acts by binding to major histocompatibility complex class II molecules and competing with MBP and other myelin proteins for such binding and presentation to T cells. Natalizumab (Tysabri) is a monoclonal antibody that binds to alpha-4-integrin on white blood cells and interferes with their movement from the bloodstream into the brain and spinal cord.

An object of the present invention is to provide a blood-based diagnostic test for a more objective, definitive, and rapid diagnosis of MS. Another object of the invention is to provide a diagnostic test for monitoring MS progression, adequacy of treatment, and/or response to treatment.

SUMMARY OF THE INVENTION

The present invention provides methods, systems, and kits for evaluating multiple sclerosis (MS) in a patient. Particularly, the invention provides convenient blood-based, gene-expression tests for evaluating MS, including for diagnosing MS, for excluding MS as a diagnosis, and for monitoring the course of disease or efficacy of treatment.

In one aspect, the invention provides a method for diagnosing MS or excluding MS as a diagnosis for a patient. In this aspect, the invention provides for a confident diagnosis of MS, or a confident exclusion of MS as a diagnosis, and in certain embodiments may help predict a clinical course of the patient's disease and/or a beneficial course of treatment.

In certain embodiments, the method comprises determining a gene expression profile for a blood sample (such as a whole blood sample) of a patient having or suspected of having MS. The gene expression profile contains gene transcript levels (or “expression levels”) for a plurality of genes that are differentially expressed in blood cells of MS patients, and such genes are listed in Tables 1 and 2. Tables 1 and 2 list genes that are differentially expressed in whole blood and PBMCs, respectively, of MS patients, and provide, inter alia, Mean-MS and Mean-control gene expression levels for these differentially expressed genes. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6 (that is, in addition to being listed in Table 1 and/or 2).

In some embodiments, the method comprises determining a gene expression profile for a white blood cell sample (such as a PBMC sample) of a patient having or suspected of having MS. In these embodiments, the gene expression profile contains gene expression levels for a plurality of genes that are differentially expressed in white blood cells of MS patients, and such genes are listed in Table 2. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6 (that is, in addition to being listed in Table 1 and/or 2).

The gene expression profile prepared according to this aspect of the invention is compared to an MS-profile and/or a non-MS profile, to classify the patient's gene expression profile as an MS profile or a non-MS profile. Generally, the non-MS profile is a healthy, non-disease, profile. In certain embodiments, the MS-profile is a relapsing-remitting MS profile.

In a second aspect, the invention provides a method for monitoring the course of disease or efficacy of treatment for an MS patient, to thereby provide accurate and objective criteria for determining disease progression and the efficacy of an MS treatment.

In this second aspect, the method comprises determining a gene expression profile, as described above, at various time points after an initial diagnosis of MS. Where the patient is undergoing treatment for MS, the gene expression profiles may include a pre-treatment (or early treatment) gene expression profile and at least one post-treatment gene expression profile of a patient having MS. In some embodiments, the MS patient is undergoing treatment with at least one of Beta-interferon, Glatiramer acetate, and Natalizumab. In certain embodiments, the pre-treatment and post-treatment gene expression profiles are determined for blood samples (such as a whole blood samples) of the patient, or white blood cell samples (such as PBMC samples). The gene expression profiles in accordance with this aspect contain gene expression levels for a plurality of genes that are differentially expressed in blood or in white blood cells of MS patients, and such genes are listed in Table 1 or 2, respectively. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6.

Further, in embodiments where the patient is undergoing treatment with Beta-Interferon, such pre- and post-treatment gene expression profiles may contain gene expression levels for the genes listed in Tables 3 and/or 5, which list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon, and which may be correlative of a positive response to treatment. In embodiments where the patient is undergoing treatment with Glatiramer acetate (e.g., Copaxone), the pre- and post-treatment profiles may contain gene expression levels for genes listed in Table 4 and/or 5, which lists genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone, and which may be correlative of a positive response to treatment. Table 5 lists genes that are differentially expressed between pre- and post-treatment with either or both of Beta-Interferon and Glatiramer acetate.

The pre-treatment gene expression profile may be compared with the post-treatment gene expression profile, to identify differences between pre-treatment and post-treatment gene expression (e.g., differences between pre-treatment and post-treatment blood transcript levels). These differences may be indicative of the patient's response (positive or negative) to treatment. Alternatively or in addition, the gene expression profiles determined over time, including the pre- and post-treatment profiles, may be compared to MS- and non-MS gene expression profiles (such as those shown in Tables 1 and 2), to determine whether, or to the extent, that the profile becomes more comparable to an MS or non-MS profile. For example, the post-treatment profile may become more or less indicative of an MS profile. Such may be indicative of a patient's positive or negative response to treatment.

In a third aspect, the invention provides a method for preparing a patient gene expression profile for evaluating MS. According to this aspect, the gene expression profile is useful for determining whether the patient has MS, as well as for monitoring the course of the disease, and predicting whether a particular treatment is or will be efficacious. In accordance with this aspect, the method generally comprises quantifying the level of expression, in a patient blood sample, for a plurality of genes listed in one of Tables 1-5.

For example, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 1 or Table 2. In some embodiments, at least one of these genes is also listed in Table 6. In accordance with this aspect, the patient may have, or be suspected to have, MS. Such gene expression profiles are useful for classifying samples as MS or non-MS samples in accordance with the first aspect of the invention, or for monitoring the course of the patient's MS over time.

Alternatively, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 3, 4, and/or 5. Preferably, at least one of these genes is also listed in Table 6. Such gene expression profiles are useful for predicting whether a particular treatment might be efficacious, or where treatment is already ongoing, determining whether the current treatment is effective.

In still other aspects, the invention provides kits and systems for performing the methods of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods, systems, and kits for evaluating multiple sclerosis (MS). The invention provides convenient blood-based, gene-expression tests for evaluating MS in patients. Such patients may be known to have MS, may be suspected of having MS on the basis of one or more MS-like symptoms or results from one or more MS-related clinical exams, or may be beginning or undergoing treatment for MS. In the various aspects of the invention, the invention aids in diagnosing MS, or excluding MS as a diagnosis, monitoring the progression of disease, and predicting or determining efficacy of the various options for MS treatment and care.

Methods For Diagnosing MS

In one aspect, the invention provides a method for diagnosing MS, or for excluding MS as a diagnosis for a patient. The method comprises determining a gene expression profile for a blood sample (such as a whole blood sample) or a white blood cell sample (such as a PBMC sample) of a patient having or suspected of having MS. The gene expression profile prepared according to this aspect of the invention is compared to an MS-profile and/or a non-MS profile, to classify the patient's gene expression profile as an MS profile or a non-MS profile. By classifying the profile as an MS or non-MS profile, a diagnosis of MS may be made, or MS may be excluded as a diagnosis.

Generally, the patient is suspected of having MS. For example, the patient may be suspected of having MS on the basis of neurologic and/or immunologic symptoms consistent with MS, e.g., after an initial physician's exam. The patient may, in some embodiments, be positive for the presence of oligoclonal bands. In these or other embodiments, the patient may have CNS lesions characteristic of MS, which are observable on an MRI. In certain embodiments, the patient has not undergone treatment for MS, but in some embodiments, the patient is already undergoing treatment, such as treatment with Beta-interferon, Glatiramer acetate, and Natalizumab.

Thus, the patient may have one or more presumptive signs of a multiple sclerosis. Presumptive signs of multiple sclerosis include for example, altered sensory, motor, visual or proprioceptive system with at least one of numbness or weakness in one or more limbs, often occurring on one side of the body at a time or the lower half of the body, partial or complete loss of vision, frequently in one eye at a time and often with pain during eye movement, double vision or blurring of vision, tingling or pain in numb areas of the body, electric-shock sensations that occur with certain head movements, tremor, lack of coordination or unsteady gait, fatigue, dizziness, muscle stiffness or spasticity, slurred speech, paralysis, problems with bladder, bowel or sexual function, and mental changes such as forgetfulness or difficulties with concentration, relative to medical standards.

The gene expression profile is determined for a blood sample, such as a whole blood sample or a white blood cell sample, of the patient. The white blood cell sample may be a Peripheral Blood Mononuclear Cell (PBMC) sample of the patient. PBMCs are a mixture of monocytes and lymphocytes. There are several known methods for isolating PBMCs from whole blood. While any suitable method may be employed, in one embodiment, PBMCs are isolated from whole blood samples using density gradient centrifugation. For example, anticoagulated whole blood is layered over a separating medium, and after centrifugation, the following layers are visually observed from top to bottom: plasma/platelets, PBMCs, separating medium and erythrocytes/granulocytes. The PBMC layer may then be removed for RNA isolation. Alternatively, the blood cell sample may be further isolated from whole blood or PBMCs to yield a cell subpopulation, such as a population of lymphocytes (e.g., T-lymphocytes or sub-population thereof). Examples for isolating such sub-populations are known in the art, and include cell sorting, or cell-capturing using antibodies to particular cell-specific markers.

In preparing the gene expression profile of the patient sample(s), RNA is extracted from the collected cells (e.g., using whole blood or PBMC samples) by any known method. For example, RNA may be purified from cells using a variety of standard procedures as described, for example, in RNA Methodologies, A laboratory guide for isolation and characterization, 2nd edition, 1998, Robert E. Farrell, Jr., Ed., Academic Press. In addition, there are various products commercially available for RNA isolation which may be used. Total RNA or polyA+ RNA may be used for preparing gene expression profiles in accordance with the invention.

The gene expression profile (or gene expression signature) is then generated for the samples using any of various techniques known in the art, and described in detail elsewhere herein. Such methods generally include, without limitation, polymerase-based assays, such as RT-PCR (e.g., Taqman™), hybridization-based assays, such as DNA microarray analysis, flap-endonuclease-based assays (e.g., Invader™), as well as direct mRNA capture with branched DNA (QuantiGene™) or Hybrid Capture™ (Digene).

The gene expression profile contains gene expression levels for a plurality of genes that are differentially expressed in blood samples of MS patients, and such genes are disclosed herein. For example, Tables 1 and 2 list genes that are differentially expressed in whole blood and PBMC samples, respectively, of MS patients. As used herein, the term “gene,” refers to a DNA sequence expressed in a sample as an RNA transcript, and may be a full-length gene (protein encoding or non-encoding) or an expressed fragment such as expressed sequence tags or “ESTs.” Thus, the sequences listed in the Tables and Sequence Listing are each independently a full-length gene sequence, whose expression product is present in samples, or is a partial expressed sequence detectable in samples, such as an EST sequence. As used herein, “differentially expressed” means that the level or abundance of an RNA transcript (or abundance of an RNA population sharing a common target sequence, such as splice variant RNAs) is significantly higher or lower in a sample as compared to a reference level. For example, the level of the RNA or RNA population may be higher or lower by at least two-fold as compared to a reference level. The reference level is the level of the same RNA or RNA population in a control sample or control population (e.g., a Mean control level).

Table 1A lists genes that are differentially expressed in whole blood of MS patients, and thus the expression level of these genes or subset thereof may be determined in patient samples to prepare a gene expression profile in accordance with this aspect of the invention. Table 1A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 1A further provides Mean-MS and Mean-control gene expression levels as generated from an exemplary sample set and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 1B lists these same genes, and expresses the differential RNA levels as fold change (Control/MS), MeanRatio (Control/MS), and Mean Difference (Control-MS).

Thus, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6.

Table 2A lists genes that are differentially expressed in PBMCs of MS patients, and thus the expression level of these genes or subset thereof may be determined in patient samples to prepare a gene expression profile in accordance with this aspect of the invention. Table 2A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 2A further provides the fold change between control and MS samples as generated from an exemplary sample set and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 2B lists these same genes, and shows the mean control and MS data signals, and indicates the top 42 genes in terms of fold change.

Thus, in accordance with these embodiments, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

In certain embodiments, the gene expression profile contains a measure of expression levels for a plurality of genes that are each, independently, expressed in MS samples relative to control samples by a fold change magnitude (up or down) of at least 1.2. In some embodiments, the plurality of genes are differentially expressed in MS samples with respect to control samples (e.g., non-MS sample) by a fold change magnitude of at least 1.5, or at least about 1.7, or at least about 2, or at least about 2.5. Alternatively, the expression levels may differ by at least about 3- or 5-, 10-fold, or more. Tables 1 and 2 list genes by differential levels of expression in control versus MS samples, as determined in whole blood or PBMCs, respectively, and such levels may be used to select genes for profiling in accordance with this paragraph.

The gene expression profile prepared according to this aspect of the invention is compared to an MS-profile and/or a non-MS profile, to classify the patient's gene expression profile as an MS profile or a non-MS profile. In certain embodiments, the non-MS profile is a healthy profile. In these or other embodiments, the MS-profile may be a general MS-profile (e.g., not limited to a clinical MS subtype), or may be a relapsing-remitting MS profile. Tables 1 and 2 present exemplary MS and non-MS profiles, which may be used to classify patient samples. Of course, additional MS and non-MS profiles for classifying samples may be generated from additional MS and control sample sets, using the genes listed in Tables 1 and 2 as described above.

Various classification schemes are known for classifying samples between two or more classes or groups, and these include, without limitation: Naïve Bayes, Support Vector Machines, Nearest Neighbors, Decision Trees, Logistic, Artificial Neural Networks, and Rule-based schemes. In addition, the predictions from multiple models can be combined to generate an overall prediction. For example, a “majority rules” prediction may be generated from the outputs of a Naïve Bayes model, a Support Vector Machine model, and a Nearest Neighbor model.

Thus, a classification algorithm or “class predictor” may be constructed to classify samples. The process for preparing a suitable class predictor is reviewed in R. Simon, Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data, British Journal of Cancer (2003) 89, 1599-1604, which review is hereby incorporated by reference in its entirety.

Generally, the gene expression profile for the patient is compared to both a non-MS profile and an MS profile. Such MS and non-MS profiles may be assembled from gene expression data disclosed herein (Tables 1 and 2), which may be stored in a database and correlated to patient profiles. Thus, MS and non-MS profiles may be assembled from data and matched to a particular patient by, for example, age, race, gender, and/or clinical manifestations of MS. The MS profile may represent a particular clinical course of MS, such as relapsing-remitting MS.

After comparing the patient's gene expression profile to the MS and/or non-MS profile, the sample is classified as, or for example, given a probability of being, an MS profile or a non-MS profile. The classification may be determined computationally based upon known methods as described above. The result of the computation may be displayed on a computer screen or presented in a tangible form, for example, as a probability (e.g., from 0 to 100%) of the patient having MS. The report will aid a physician in diagnosis or treatment of the patient. For example, in certain embodiments of the invention, the patient's gene expression profile will be determined to be an MS profile on the basis of a probability, and the patient will be subsequently treated for MS as appropriate. In other embodiments, the patient's profile will be determined to be a non-MS profile, thereby allowing the physician to exclude MS as a diagnosis for the patient.

In various embodiments, the method according to this aspect of the invention distinguishes a MS-afflicted patient from a non-MS afflicted patient with at least about 50%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater accuracy. In this respect, the method according to this aspect may lend additional or alternative predictive value over standard clinical methods of diagnosing MS, such as for example, absence or presence of lesions on an MRI, testing positive or negative for oligoclonal bands, or the absence or presence of other signs and symptoms of MS such as blurred vision, fatigue, and/or loss of balance.

Methods For Determining Efficacy of Treatment

In a second aspect, the invention is a method for monitoring treatment of an MS patient. While any treatment program may be monitored, including test compounds, in certain embodiments the patient is undergoing treatment with one or more of Beta-Interferon, Glatiramer acetate, and Natalizumab. In this aspect, the invention comprises determining a pre-treatment (or early treatment) gene expression profile and at least one post-treatment gene expression profile for the patient, as already described. The pre-treatment profile may be determined from a sample taken prior to treatment, or may be an early treatment profile determined, for example, for a sample taken within the first six months of treatment. The post-treatment profile(s) may be determined for samples taken anytime after the start of treatment, such as after about three months, after about six months, after about twelve months of treatment, and/or later.

The pre-treatment and post-treatment gene expression profiles are prepared from blood samples (e.g., whole blood) or white blood cell samples (such as PBMC samples or subpopulation thereof), isolated from the patient at the selected pre- and post-treatment time points.

The pre- and post-treatment gene expression profiles contain gene expression levels for a plurality of genes that are differentially expressed in blood cells of MS patients, as described in the preceding section with respect to Tables 1, 2, and 6. Thus, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6. Alternatively, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

Thus, such gene expression profiles may be useful for monitoring a patient's treatment, to determine whether the post-treatment sample classifies as an MS-sample, to the same, lesser, or greater extent as the pre-treatment sample. Such pre-treatment and post-treatment samples may be classified or scored as MS or non-MS samples as disclosed elsewhere herein.

Alternatively, or in addition, the pre-treatment and post-treatment gene expression profiles may be compared to identify differences in gene expression upon treatment with MS. For example, where the patient is being treated with Beta-interferon, gene expression values may be determined (pre- and post-treatment) for genes (e.g., 3, 5, 7, 10, 15, 20, or 40 genes) listed in Tables 3 and/or 5. In certain embodiments, at least one gene is also listed in Table 6, in addition to being listed in Tables 3 and/or 5. Or, where the patient is being treated with Glatiramer acetate, gene expression values may be determined (pre- and post-treatment) for genes (e.g., 3, 5, 7, 10, 15, 20, or 40 genes) listed in Tables 4 or 5. In certain embodiments, at least one gene is also listed in Table 6, in addition to being listed in Tables 3 and/or 5. Tables 3 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon. Table 4 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone. Table 5 lists genes that are differentially expressed between pre- and post-treatment with each of Beta-Interferon and Glatiramer acetate.

The pre-treatment gene expression profile may then be compared with the post-treatment gene expression profile, to identify differences between pre-treatment and post-treatment gene expression. These differences may be indicative of the patient's response (positive or negative) to treatment.

Many of the genes that are indicative of a patient's response to Beta-interferon may encode cell surface markers, e.g. cell surface markers on immune cells, and several of which are interferon-inducible genes (see Table 3). Accordingly, in some embodiments of the invention, at least one, or at least five, or at least 10 of the genes in the gene expression profile encode a cell-surface marker, some or all of which are interferon-inducible. Such genes are listed in Example 2, herein.

After comparison, the post-treatment gene expression profile may be classified as being indicative of MS, or not being indicative of MS (or being less indicative of MS than the pre-treatment sample), for example due to effective therapy. Alternatively, the post-treatment sample may be more indicative of MS, suggesting that an alternative therapy would be desirable. The analysis in accordance with this aspect may be performed computationally as described. The result of the analysis may be displayed or presented in tangible form to aid in considering further treatment options, such as adjusting or changing the treatment, if needed, and to track the clinical course of the patient's disease.

Methods for Preparing Gene Expression Profiles

In a third aspect, the invention provides a method for preparing a patient gene expression profile for evaluating MS. According to this aspect, the gene expression profile is useful for determining whether the patient has MS, as well as for monitoring the course of the disease, and predicting whether a particular treatment is or will be efficacious. In accordance with this aspect, the method generally comprises quantifying the level of expression, in a patient blood sample, for a plurality of genes listed in one of Tables 1-5 as discussed above for the first and second aspects of the invention.

For example, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 1 or Table 2. In some embodiments, at least one of these genes is also listed in Table 6. In accordance with this aspect, the patient may have, or be suspected to have, MS. Such gene expression profiles are useful for classifying samples as MS or non-MS samples in accordance with the first aspect of the invention, or for monitoring the course of the patient's MS over time.

Specifically, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6.

Alternatively, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

Alternatively, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 3, 4, and/or 5. Preferably, at least one of these genes is also listed in Table 6. Such gene expression profiles are useful for predicting whether a particular treatment might be efficacious, or where treatment is already ongoing, determining whether the current treatment is effective.

Assay Formats

Gene expression profiles, including patient gene expression profiles and the MS and non-MS profiles as described herein, may be prepared according to any suitable method for measuring gene expression. That is, the profiles may be prepared using any quantitative or semi-quantitative method for determining RNA transcript levels in samples. Such methods include polymerase-based assays, such as RT-PCR, Taqman™, hybridization-based assays, for example using DNA microarrays or other solid support, nucleic acid sequence based amplification (NASBA), flap endonuclease-based assays, as well as direct mRNA capture with branched DNA (QuantiGene™) or Hybrid Capture™ (Digene). The assay format, in addition to determining the gene expression levels for a combination of genes listed in one or more of Tables 1-6, will also allow for the control of, inter alia, intrinsic signal intensity variation between tests. Such controls may include, for example, controls for background signal intensity and/or sample processing, and/or other desirable controls for gene expression quantification across samples. For example, expression levels between samples may be controlled by testing for the expression level of one or more genes that are not differentially expressed in MS patients, or which are generally expressed at similar levels across the population. Such genes may include constitutively expressed genes, many of which are known in the art. Exemplary assay formats for determining gene expression levels, and thus for preparing gene expression profiles and MS- and non-MS profiles are described in this section.

The nucleic acid sample is typically in the form of mRNA or reverse transcribed mRNA (cDNA) isolated from a blood sample, such as a whole blood sample, PBMC sample, or other subpopulation of blood cells (e.g., T-lymphocytes) isolated from the patient's blood. In some embodiments, the nucleic acids in the sample may be cloned or amplified, generally in a manner that does not bias the representation of the transcripts within a sample. In some embodiments, it may be preferable to use total RNA or polyA+ RNA as a source without cloning or amplification, to avoid additional processing steps.

As is apparent to one of skill in the art, nucleic acid samples used in the methods of the invention may be prepared by any available method or process. Methods of isolating total mRNA are well known to those of skill in the art. For example, methods of isolation and purification of nucleic acids are described in detail in Chapter 3 of Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24, Hybridization With Nucleic Acid Probes: Theory and Nucleic Acid Probes, P. Tijssen, Ed., Elsevier Press, New York, 1993. Such samples include RNA samples, but also include cDNA synthesized from a mRNA sample isolated from a cell or tissue of interest (e.g., whole blood or PBMC sample). Such samples also include DNA amplified from the cDNA, and RNA transcribed from the amplified DNA.

In determining a patient's gene expression profile, or in determining an MS- or non-MS profile in accordance with the invention, a hybridization-based assay may be employed. Nucleic acid hybridization involves contacting a probe and a target sample under conditions where the probe and its complementary target sequence (if present) in the sample can form stable hybrid duplexes through complementary base pairing. The nucleic acids that do not form hybrid duplexes may be washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids may be denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids. Under low stringency conditions (e.g., low temperature and/or high salt) hybrid duplexes (e.g., DNA:DNA, RNA:RNA, or RNA:DNA) will form even where the annealed sequences are not perfectly complementary. Thus, specificity of hybridization is reduced at lower stringency. Conversely, at higher stringency (e.g., higher temperature or lower salt) successful hybridization tolerates fewer mismatches. One of skill in the art will appreciate that hybridization conditions may be selected to provide any degree of stringency.

In certain embodiments, hybridization is performed at low stringency, such as 6×SSPET at 37° C. (0.005% Triton X-100), to ensure hybridization, and then subsequent washes are performed at higher stringency (e.g., 1×SSPET at 37° C.) to eliminate mismatched hybrid duplexes. Successive washes may be performed at increasingly higher stringency (e.g., down to as low as 0.25×SSPET at 37° C. to 50° C.) until a desired level of hybridization specificity is obtained. Stringency can also be increased by addition of agents such as formamide. Hybridization specificity may be evaluated by comparison of hybridization to the test probes with hybridization to the various controls that may be present, as described below (e.g., expression level control, normalization control, mismatch controls, etc.).

In general, there is a tradeoff between hybridization specificity (stringency) and signal intensity. Thus, in a preferred embodiment, the wash is performed at the highest stringency that produces consistent results and that provides a signal intensity greater than approximately 10% of the background intensity. The hybridized array may be washed at successively higher stringency solutions and read between each wash. Analysis of the data sets thus produced will reveal a wash stringency above which the hybridization pattern is not appreciably altered and which provides adequate signal for the particular oligonucleotide probes of interest.

The hybridized nucleic acids are typically detected by detecting one or more labels attached to the sample nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art. See WO 99/32660.

Numerous hybridization assay formats are known, and which may be used in accordance with the invention. Such hybridization-based formats include solution-based and solid support-based assay formats. Solid supports containing oligonucleotide probes designed to detect differentially expressed genes (e.g., listed in Tables 1-5) can be filters, polyvinyl chloride dishes, particles, beads, microparticles or silicon or glass based chips, etc. Any solid surface to which oligonucleotides can be bound, either directly or indirectly, either covalently or non-covalently, may be used. Bead-based assays are described, for example, in U.S. Pat. Nos. 6,355,431, 6,396,995, and 6,429,027, which are hereby incorporated by reference. Other chip-based assays are described in U.S. Pat. Nos. 6,673,579, 6,733,977, and 6,576,424, which are hereby incorporated by reference.

An exemplary solid support is a high density array or DNA chip, which may contain a particular oligonucleotide probes at predetermined locations on the array. Each predetermined location may contain more than one molecule of the probe, but each molecule within the predetermined location has an identical probe sequence. Such predetermined locations are termed features. Probes corresponding to the genes of Tables 1-5 may be attached to single or multiple solid support structures, e.g., the probes may be attached to a single chip or to multiple chips to comprise a chip set.

Oligonucleotide probe arrays for expression monitoring can be made and used according to any techniques known in the art (see for example, Lockhart et al (1996), Nat Biotechnol 14:1675-1680; McGall et al. (1996), Proc Nat Acad Sci USA 93:13555-13460). Such probe arrays may contain the oligonucleotide probes necessary for determining a patient's gene expression profile, or for preparing MS- and non-MS profiles with population samples. Thus, such arrays may contain oligonucleotide designed to hybridize to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 70, 100, 200, 300 or more of the genes described herein (e.g., as described in one of Tables 1-5, or as described in any of Tables 1-5). In some embodiments, the array contains probes designed to hybridize to all or nearly all of the genes listed in Tables 1-5. In still other embodiments, arrays are constructed that contain oligonucleotides designed to detect all or nearly all of the genes in Table 1-5 on a single solid support substrate, such as a chip or a set of beads.

Probes based on the sequences of the genes described herein for preparing expression profiles may be prepared by any suitable method. Oligonucleotide probes, for hybridization-based assays, will be of sufficient length or composition (including nucleotide analogs) to specifically hybridize only to appropriate, complementary nucleic acids (e.g., exactly or substantially complementary RNA transcripts or cDNA). Typically the oligonucleotide probes will be at least about 10, 12, 14, 16, 18, 20 or 25 nucleotides in length. In some cases, longer probes of at least 30, 40, or 50 nucleotides may be desirable. In some embodiments, complementary hybridization between a probe nucleic acid and a target nucleic acid embraces minor mismatches (e.g., one, two, or three mismatches) that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence. Of course, the probes may be perfect matches with the intended target probe sequence, for example, the probes may each have a probe sequence that is perfectly complementary to a target sequence (e.g., a sequence of a gene listed in Tables 1-5).

A probe is a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. A probe may include natural (i.e., A, G, U, C, or T) or modified bases (7-deazaguanosine, inosine, etc.), or locked nucleic acid (LNA). In addition, the nucleotide bases in probes may be joined by a linkage other than a phosphodiester bond, so long as the bond does not interfere with hybridization. Thus, probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages.

When using hybridization-based assays, in may be necessary to control for background signals. The terms “background” or “background signal intensity” refer to hybridization signals resulting from non-specific binding, or other interactions, between the labeled target nucleic acids and components of the oligonucleotide array (e.g., the oligonucleotide probes, control probes, the array substrate, etc.). Background signals may also be produced by intrinsic fluorescence of the array components themselves. A single background signal can be calculated for the entire array, or a different background signal may be calculated for each location of the array. In an exemplary embodiment, background is calculated as the average hybridization signal intensity for the lowest 5% to 10% of the probes in the array. Alternatively, background may be calculated as the average hybridization signal intensity produced by hybridization to probes that are not complementary to any sequence found in the sample (e.g. probes directed to nucleic acids of the opposite sense or to genes not found in the sample such as bacterial genes where the sample is mammalian nucleic acids). Background can also be calculated as the average signal intensity produced by regions of the array that lack any probes at all. Of course, one of skill in the art will appreciate that hybridization signals may be controlled for background using one or a combination of known approached, including one or a combination of approaches described in this paragraph.

The hybridization-based assay will be generally conducted under conditions in which the probe(s) will hybridize to their intended target subsequence, but with only insubstantial hybridization to other sequences or to other sequences, such that the difference may be identified. Such conditions are sometimes called “stringent conditions.” Stringent conditions are sequence-dependent and can vary under different circumstances. For example, longer probe sequences generally hybridize to perfectly complementary sequences (over less than fully complementary sequences) at higher temperatures. Generally, stringent conditions may be selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Exemplary stringent conditions may include those in which the salt concentration is at least about 0.01 to 1.0 M Na⁺ ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides). Desired hybridization conditions may also be achieved with the addition of agents such as formamide or tetramethyl ammonium chloride (TMAC).

When using an array, one of skill in the art will appreciate that an enormous number of array designs are suitable for the practice of this invention. The array will typically include a number of test probes that specifically hybridize to the sequences of interest. That is, the array will include probes designed to hybridize to any region of the genes listed in Tables 1-5, and the accompanying sequence listing. In instances where the gene reference in the Tables is an EST, probes may be designed from that sequence or from other regions of the corresponding full-length transcript that may be available in any of the public sequence databases, such as those herein described. See WO 99/32660 for methods of producing probes for a given gene or genes. In addition, software is commercially available for designing specific probe sequences. Typically, the array will also include one or more control probes, such as probes specific for a constitutively expressed gene, thereby allowing data from different arrays to be normalized or controlled.

The hybridization-based assays may include, in addition to “test probes” (e.g., that bind the target sequences of interest, which are listed in Tables 1-6), the assay may also test for hybridization to one or a combination of control probes. Exemplary control probes include: normalization controls, expression level controls, and mismatch controls. For example, when determining the levels of gene expression in patient or control samples, the expression values may be normalized to control between samples. That is, the levels of gene expression in each sample may be normalized by determining the level of expression of at least one constitutively expressed gene in each sample. In accordance with the invention, the constitutively expressed gene is generally not differentially expressed in samples (blood samples, including whole blood or PBMC samples) of MS patients.

Other useful controls are normalization controls, for example, using probes designed to be complementary to a labeled reference oligonucleotide added to the nucleic acid sample to be assayed. The signals obtained from the normalization controls after hybridization provide a control for variations in hybridization conditions, label intensity, “reading” efficiency and other factors that may cause the signal of a perfect hybridization to vary between arrays. In one embodiment, signals (e.g., fluorescence intensity) read from all other probes in the array are divided by the signal (e.g., fluorescence intensity) from the control probes thereby normalizing the measurements. Exemplary normalization probes are selected to reflect the average length of the other probes (e.g., test probes) present in the array, however, they may be selected to cover a range of lengths. The normalization control(s) may also be selected to reflect the (average) base composition of the other probes in the array. In some embodiments, the assay employs one or a few normalization probes, and they are selected such that they hybridize well (i.e., no secondary structure) and do not hybridize to any potential targets.

The hybridization-based assay may employ expression level controls, for example, probes that hybridize specifically with constitutively expressed genes in the biological sample. Virtually any constitutively expressed gene provides a suitable target for expression level controls. Typically expression level control probes have sequences complementary to subsequences of constitutively expressed “housekeeping genes” including, but not limited to the actin gene, the transferrin receptor gene, the GAPDH gene, and the like.

The hybridization-based assay may also employ mismatch controls for the target sequences, and/or for expression level controls or for normalization controls. Mismatch controls are probes designed to be identical to their corresponding test or control probes, except for the presence of one or more mismatched bases. A mismatched base is a base selected so that it is not complementary to the corresponding base in the target sequence to which the probe would otherwise specifically hybridize. One or more mismatches are selected such that under appropriate hybridization conditions (e.g., stringent conditions) the test or control probe would be expected to hybridize with its target sequence, but the mismatch probe would not hybridize (or would hybridize to a significantly lesser extent). Preferred mismatch probes contain a central mismatch. Thus, for example, where a probe is a 20-mer, a corresponding mismatch probe will have the identical sequence except for a single base mismatch (e.g., substituting a G, a C or a T for an A) at any of positions 6 through 14 (the central mismatch).

Mismatch probes thus provide a control for non-specific binding or cross hybridization to a nucleic acid in the sample other than the target to which the probe is directed. For example, if the target is present, the perfect match probes should provide a more intense signal than the mismatch probes. The difference in intensity between the perfect match and the mismatch probe helps to provide a good measure of the concentration of the hybridized material.

Methods of forming high density arrays of oligonucleotides with a minimal number of synthetic steps are known. The oligonucleotide analogue array can be synthesized on a single or on multiple solid substrates by a variety of methods, including, but not limited to, light-directed chemical coupling, and mechanically directed coupling (see Pirrung, U.S. Pat. No. 5,143,854). In brief, the light-directed combinatorial synthesis of oligonucleotide arrays on a glass surface proceeds using automated phosphoramidite chemistry and chip masking techniques. In one specific implementation, a glass surface is derivatized with a silane reagent containing a functional group, e.g., a hydroxyl or amine group blocked by a photolabile protecting group. Photolysis through a photolithographic mask is used selectively to expose functional groups which are then ready to react with incoming 5′ photoprotected nucleoside phosphoramidites. The phosphoramidites react only with those sites which are illuminated (and thus exposed by removal of the photolabile blocking group). Thus, the phosphoramidites only add to those areas selectively exposed from the preceding step. These steps are repeated until the desired array of sequences have been synthesized on the solid surface. Combinatorial synthesis of different oligonucleotide analogues at different locations on the array is determined by the pattern of illumination during synthesis and the order of addition of coupling reagents.

In addition to the foregoing, additional methods which can be used to generate an array of oligonucleotides on a single substrate are described in PCT Publication Nos. WO 93/09668 and WO 01/23614. High density nucleic acid arrays can also be fabricated by depositing pre-made or natural nucleic acids in predetermined positions. Synthesized or natural nucleic acids are deposited on specific locations of a substrate by light directed targeting and oligonucleotide directed targeting. Another embodiment uses a dispenser that moves from region to region to deposit nucleic acids in specific spots.

The hybdridization-based assay may, as an alternative to purely passive hybridization, employ the methods described in U.S. Pat. No. 6,326,173, which is hereby incorporated by reference. For example, the assay may involve electronically concentrating and hybridizing the nucleic acid sample to the surface of a microchip (e.g., capture sites). This method may allow for rapid concentration and subsequent specific hybridization of template nucleic acid molecules to their complementary anchored amplification primers.

Alternatively, the invention may employ reverse transcription polymerase chain reaction (RT-PCR), which is a sensitive method for the detection of mRNA, including low abundant mRNAs present in clinical samples. The application of fluorescence techniques to RT-PCR combined with suitable instrumentation has led to quantitative RT-PCR methods that combine amplification, detection and quantification in a closed system. Two commonly used quantitative RT-PCR techniques are the Taqman RT-PCR assay (ABI, Foster City, USA) and the Lightcycler assay (Roche, USA).

Thus, in one embodiment of the present invention, the preparation of patient gene expression profiles or the preparation of MS- and non-MS profiles comprises conducting real-time quantitative PCR (TaqMan) with sample-derived RNA and control RNA. Holland, et al., PNAS 88:7276-7280 (1991) describe an assay known as a Taqman assay. The 5′ to 3′ exonuclease activity of Taq polymerase is employed in a polymerase chain reaction product detection system to generate a specific detectable signal concomitantly with amplification. An oligonucleotide probe, non-extendable at the 3′ end, labeled at the 5′ end, and designed to hybridize within the target sequence, is introduced into the polymerase chain reaction assay. Annealing of the probe to one of the polymerase chain reaction product strands during the course of amplification generates a substrate suitable for exonuclease activity. During amplification, the 5′ to 3′ exonuclease activity of Taq polymerase degrades the probe into smaller fragments that can be differentiated from undegraded probe. A version of this assay is also described in Gelfand et al., in U.S. Pat. No. 5,210,015, which is hereby incorporated by reference.

Further, U.S. Pat. No. 5,491,063 to Fisher, et al., which is hereby incorporated by reference, provides a Taqman-type assay. The method of Fisher et al. provides a reaction that results in the cleavage of single-stranded oligonucleotide probes labeled with a light-emitting label wherein the reaction is carried out in the presence of a DNA binding compound that interacts with the label to modify the light emission of the label. The method of Fisher uses the change in light emission of the labeled probe that results from degradation of the probe.

The TaqMan detection assays offer certain advantages. First, the methodology makes possible the handling of large numbers of samples efficiently and without cross-contamination and is therefore adaptable for robotic sampling. As a result, large numbers of test samples can be processed in a very short period of time using the TaqMan assay. Another advantage of the TaqMan system is the potential for multiplexing. Since different fluorescent reporter dyes can be used to construct probes, the expression of several different genes associated with MS could be assayed in the same PCR reaction, thereby reducing the labor costs that would be incurred if each of the tests were performed individually. Thus, the TaqMan assay format is preferred where the patient's gene expression profile, and the corresponding MS- and non-MS profiles comprise the expression levels of about 20 of fewer, or about 10 or fewer, or about 7 of fewer, or about 5 genes (e.g., genes listed in Tables 1-6).

Alternatively, the assay format may employ the methodologies described in Direct Multiplexed Measurement of Gene Expression with Color-Coded Probe Pairs, Nature Biotechnology (Mar. 7, 2008), which describes the nCounter™ Analysis System (nanoString Technologies). This system captures and counts individual mRNA transcripts by a molecular bar-coding technology, and is commercialized by Nanostring.

In other embodiments, the invention employs detection and quantification of RNA levels in real-time using nucleic acid sequence based amplification (NASBA) combined with molecular beacon detection molecules. NASBA is described for example, in Compton J., Nucleic acid sequence-based amplification, Nature 1991; 350(6313): 91-2. NASBA is a singe-step isothermal RNA-specific amplification method. Generally, the method involves the following steps: RNA template is provided to a reaction mixture, where the first primer attaches to its complementary site at the 3′ end of the template; reverse transcriptase synthesizes the opposite, complementary DNA strand; RNAse H destroys the RNA template (RNAse H only destroys RNA in RNA-DNA hybrids, but not single-stranded RNA); the second primer attaches to the 3′ end of the DNA strand, and reverse transcriptase synthesizes the second strand of DNA; and T7 RNA polymerase binds double-stranded DNA and produces a complementary RNA strand which can be used again in step 1, such that the reaction is cyclic.

In yet other embodiments, the assay format is a flap endonuclease-based format, such as the Invader™ assay (Third Wave Technologies). In the case of using the invader method, an invader probe containing a sequence specific to the region 3′ to a target site, and a primary probe containing a sequence specific to the region 5′ to the target site of a template and an unrelated flap sequence, are prepared. Cleavase is then allowed to act in the presence of these probes, the target molecule, as well as a FRET probe containing a sequence complementary to the flap sequence and an auto-complementary sequence that is labeled with both a fluorescent dye and a quencher. When the primary probe hybridizes with the template, the 3′ end of the invader probe penetrates the target site, and this structure is cleaved by the Cleavase resulting in dissociation of the flap. The flap binds to the FRET probe and the fluorescent dye portion is cleaved by the Cleavase resulting in emission of fluorescence.

In yet other embodiments, the assay format employs direct mRNA capture with branched DNA (QuantiGene™, Panomics) or Hybrid Capture™ (Digene).

The design of appropriate probes for hybridizing to a particular target nucleic acid, and as configured for any appropriate nucleic acid detection assay, is well known.

Computer Systems

In another aspect, the invention is a computer system that contains a database, on a computer-readable medium, of mean gene expression values determined in an MS patient population and in a non-MS patient population. These gene expression values are determined in blood samples, such as whole blood cell samples or white blood cell samples (e.g., PBMC samples), and for genes selected from one or more of Tables 1-5. The database may include gene expression measurements for at least one or a plurality of genes that are also listed in Table 6. The database may include, for each gene, Mean-MS and Mean-Control (e.g., non-MS or healthy) gene expression levels, as well as various statistical measures, including measures of value dispersion (e.g., Standard Variation), fold change (e.g., between control and MS populations), and statistical significance (statistical association with MS). Various such measures are shown in the accompanying Tables, and such measures may be employed in the computer systems of the invention. Further, the MS patient population may include patients being treated with Beta-interferon, Glatiramer acetate, and/or Natalizumab, and such treatment and other clinical information may be included in the database such that an appropriate gene expression profile may be assembled for use with the diagnostic methods of the invention. Generally, profiles may be assembled based upon parameters to be selected and input by a user, with these parameters including one or more of age, race, gender, MS treatment, and clinical manifestation and course of MS.

In certain embodiments, the database contains mean gene expression values for at least about 5, 7, 10, 20, 40, 50, or 100 genes selected from any one, or a combination of, Tables 1-6. In some embodiments, the database may contain mean gene expression values for more than about 100 genes, or about 300 genes, or about 400 genes selected from Tables 1-6. In one embodiment, the database contains mean gene expression values for all or substantially all the genes listed in Tables 1-6. The database may include gene expression measurements for at least one or a plurality of genes that are also listed in Table 6.

The computer system of the invention may be programmed to compare (e.g., in response to user inputs) a gene expression profile to a non-MS gene expression profile and/or an MS-gene expression profile stored and/or generated from the database, to determine whether the gene expression profile is itself an MS-profile or a non-MS profile. For example, the computer system may be programmed to perform any of the known classification schemes for classifying gene expression profiles. Various classification schemes are known for classifying samples, and these include, without limitation: Naïve Bayes, Support Vector Machines, Nearest Neighbors, Decision Trees, Logistic, Artificial Neural Networks, and Rule-based schemes. The computer system may employ a classification algorithm or “class predictor” as described in R. Simon, Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data, British Journal of Cancer (2003) 89, 1599-1604, which is hereby incorporated by reference in its entirety.

The computer system of the invention may comprise a user interface, allowing a user to input gene expression values for comparison to an MS and/or non-MS gene expression profile, or gene expression profile previously generated for the patient. The patient's gene expression values may be input from a location remote from the database.

The computer system may further comprise a display, for presenting and/or displaying a result, such as a profile assembled from the database, or the result of a comparison (or classification) between input gene expression values and an MS and non-MS profiles. Such results may further be provided in a tangible form (e.g., as a printed report).

The computer system of the invention may further comprise relational databases containing sequence information, for instance, for the genes of Tables 1-5. For example, the database may contain information associated with a given gene, or patient sample, such as descriptive information about the gene associated with the sequence information, or descriptive information concerning the clinical status of the patient. The database may be designed to include different parts, for instance a sequence database and a gene expression database. Methods for the configuration and construction of such databases and computer-readable media to which such databases are saved are widely available, for instance, see U.S. Pat. No. 5,953,727, which is hereby incorporated by reference in its entirety.

The databases of the invention may be linked to an outside or external database (e.g., on the world wide web) such as GenBank (ncbi.nlm.nih.gov/entrez.index.html); KEGG (genome.ad.jp/kegg); SPAD (grt.kuyshu-u.ac.jp/spad/index.html); HUGO (gene.ucl.ac.uk/hugo); Swiss-Prot (expasy.ch.sprot); Prosite (expasy.ch/tools/scnpsitl.html); OMIM (ncbi.nlm.nih.gov/omim); and GDB (gdb.org). In certain embodiments, the external database is GenBank and the associated databases maintained by the National Center for Biotechnology Information (NCBI) (ncbi.nlm.nih.gov).

Any appropriate computer platform, user interface, etc. may be used to perform the necessary comparisons between sequence information, gene expression information (e.g., gene expression profiles) and any other information in the database or information provided as an input. For example, a large number of computer workstations are available from a variety of manufacturers, such has those available from Silicon Graphics. Client/server environments, database servers and networks are also widely available and appropriate platforms for the databases described herein.

The databases of the invention may be used to produce, among other things, electronic Northerns that allow the user to determine the samples in which a given gene is expressed and to allow determination of the abundance or expression level of the given gene.

Diagnostic Kits

The invention further provides a kit or array containing nucleic acid primers and/or probes for determining the level of expression in a patient sample of a plurality of genes listed in Tables 1-5. The kit may consist essentially of primers and/or probes related to evaluating MS in a sample, and primers and/or probes related to necessary or meaningful assay controls (such as expression level controls and normalization controls, as described herein under “Assay Formats”). The kit for evaluating MS may comprise nucleic acid probes and/or primers designed to detect the expression level of ten or more genes associated with MS, such as the genes listed in Tables 1, 2, 3, 4, and/or 5. The kit may include a set of probes and/or primers designed to detect or quantify the expression levels of at least 5, 7, 10, or 20 genes listed in one or more of Tables 1, 2, 3, 4, and/or 5. In certain embodiments, the kit includes at least one probe and/or primer for quantifying expression of at least one or a plurality of genes that are also listed in Table 6. The primers and/or probes may be designed to detect gene expression levels in accordance with any assay format, including those described herein under the heading “Assay Format.” Exemplary assay formats include polymerase-based assays, such as RT-PCR, Taqman™, hybridization-based assays, for example using DNA microarrays or other solid support, nucleic acid sequence based amplification (NASBA), flap endonuclease-based assays.

In accordance with this aspect, the probes and primers may comprise antisense nucleic acids or oligonucleotides that are wholly or partially complementary to the diagnostic targets described herein (e.g., Tables 1-6). The probes and primers will be designed to detect the particular diagnostic target via an available nucleic acid detection assay format, which are well known in the art. The kits of the invention may comprise probes and/or primers designed to detect the diagnostic targets via detection methods that include amplification, endonuclease cleavage, and hybridization.

Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods.

EXAMPLES

MS and control (non-MS) gene expression profiles were identified by hybridization of RNA samples (from whole blood or PBMC samples) to microarrays.

Total RNA isolated from PBMC samples of 11 MS patients and 8 healthy controls was hybridized to a U133A/B chip set (Affymetrix).

Total RNA isolated from whole blood of 62 MS patients and 64 healthy controls was hybridized to a U133 Plus 2.0 chip (Affymetrix). These patients had at least one diagnosis of relapsing remitting MS.

Samples were processed as follows.

For PBMC isolation and subsequent RNA isolation, whole blood was collected into Vacutainer tubes (BD) containing an anticoagulant such as heparin. Peripheral blood mononuclear cells (PBMCs) were isolated by ficoll-hypaque density gradient centrifugation. Total RNA was isolated using standard RNA isolation kits (Qiagen).

For whole blood and subsequent RNA isolation, approximately 2.5 ml of whole blood was collected into each of 2-4 PAXgene tubes (BD/PreAnalytiX) using a blood collection set (BD Safety-Lok™ Blood Collection Set with butterfly needle), per PAXgene tube) following the protocol recommended by the manufacture. The PAXgene tubes were inverted 8-10 times to ensure proper mixture of blood with RNA stabilization solution. Total RNA was isolated using the PAXgene 96 Blood RNA Kit (Qiagen).

Following RNA isolation, the RNA was checked for quality, quantity and purity. Total RNA was evaluated for Quality by using the Agilent Bioanalyzer. RNA preps were quantified by measuring the absorbance at A260 and purity was assessed based on the ratio of the absorbance at A260/A280.

Hybridization of total RNA to microarrays, and following analysis of the data, produced the following MS and non-MS gene expression profiles (or “signatures”).

Table 1A lists genes that are differentially expressed in whole blood of MS patients, and provides an exemplary MS and non-MS profile for such genes. Table 1A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 1A further provides Mean-MS and Mean-control gene expression levels as generated from the sample and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 1B lists these same genes, and expresses the differential RNA levels as fold change (Control/MS).

Table 2A lists genes that are differentially expressed in PBMCs of MS patients, and provides an exemplary MS and non-MS profile for such genes. Table 2A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 2A further provides the fold change between control and MS samples as generated from this exemplary sample and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 2B lists these same genes, and shows the mean control and MS data signals, and indicates the top 42 genes in terms of fold change.

Tables 3 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon. Table 4 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone. Table 5 lists genes that are differentially expressed between pre- and post-treatment with each of Beta-Interferon and Glatiramer acetate.

The identification of such gene signatures, is illustrated in the following examples.

Example 1 Genes that are Differentially Expressed Between MS and Normal Samples Using a False Discovery Rate P-Value of 0.001.

The procedure to derive the list of differentially expressed genes in Table 2 was as follows.

A Genesis® (GeneLogic proprietary software) Comparative Analysis was performed using normal white blood cell (WBC) samples as the reference set and MS WBC samples as the experimental set. Parameters were as follows:

-   -   Log with Floor=0,     -   95% Confidence level,     -   Unequal Variance,     -   Exclude Expression with Call Values of “Unknown” or “No Value,”     -   Sample Set Expression Lower and Upper Percentiles of 25 and 75,     -   MAS5.0 Affymetrix Summarization,     -   Exclude gene fragments absent in all samples,

No other analysis filters were used. The analysis yielded 25,340 gene fragments. Fold Change, t-test p-value, and all sample expression values for each of these 25,340 fragments were exported from Genesis. All MAS5 logged expression values from Genesis for the 25,340 gene fragments for all 19 samples were uploaded into Partek Genomics Suite(R) software. A Benjamini and Hochberg False Discovery Rate correction was performed using a p-value cutoff of 0.001. This yielded a set of 339 non-control gene fragments listed in Table 2. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

A correlation heatmap was calculated and visualized using Stat->Correlate->Similarity Matrix. Parameters=Pearson, All Combinations (19×19). The default heatmap showed the following. First, the normal (Control) group is cohesive and highly correlated. Second, the MS within-group correlations were higher than the Normal within-group correlations, except for three MS samples. These three MS samples were not as highly correlated to the remainder of the MS samples as the correlations for the majority of this group's intersample correlations. However, the three samples in question are also not highly correlated to each other, indicating absence of “batch” effect for contiguous GID's. Third, the Normal vs. MS correlations indicate robust differences even before gene selection, a sign that many genes are differentially expressed between the groups. Fourth, correlations are at levels consistent with what is expected. No outliers.

The data was transposed in Partek to allow for Principal Components Analysis (PCA). A categorical factor variable was added to the transposed data for coloring the PCA visual by terms “MS” and “Normal”. PCA Parameters: Correlation Dispersion Matrix, Normalized Eigenvector Scaling. Review of PCA showed: the variance explained by the plot is relatively larger than expected such that a robust response is expected upon hypothesis testing for individual genes. Even without prior gene selection, both groups separate well on the 1^(st) principal component, indicating a robust separation of samples. Further, the number of fragments p<0.01 (unadjusted) was 4,146, and the number of fragments p<0.01 (unadjusted) and with a fold change of >=2 was 386. This number of changing fragments indicates a high degree of regulation that is likely to be biologically real.

Comparison of the genes and gene fragments listed in Table 2 between baseline MS samples and control blood samples identifies a differentiating signature.

Thus, genes were further identified on the basis of stringent statistical differentiation thresholding, for example, using a fold-change cut-off to identify gene fragments with expression intensity in MS WBC that is either less than half or more than twice the expression intensity in normal WBC. This rationale is based on the consideration that it is more practical to detect changes in clinical samples when the range of the difference between disease and normal is large.

The procedure to derive the list of gene fragments with a fold change of at least 2 was as follows. A Genesis® Comparative Analysis was performed using normal WBC samples as the reference set and MS WBC samples as the experimental set. Parameters were as follows:

-   -   Log with Floor=0,     -   95% Confidence level,     -   Unequal Variance,     -   Exclude expression with call values of “unknown” or “no value,”     -   MAS5.0 Affymetrix Summarization,     -   Include only gene fragments that do not have Affymetrix         “Present” Call in 100% of Samples in either sample set,     -   Sample set expression lower and upper percentiles of 25 and 75,     -   Fold-change magnitude of +/−2.0,     -   Raw p-value threshold of 0.05.

This analysis yielded a set of 182 genes, which are listed in Table 2. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

Thus comparison of the genes listed in Table 2 between baseline MS samples and control blood samples identifies a differentiating signature.

Example 2 Genes that are Differentially Expressed Between Pre- and Post-Avonex Treatment MS Samples

Expression changes in WBC after treatment can be used as a pharmacodynamic measure of exposure to drugs, and thus as a measure of adequate dosing. They may also be a measure of therapeutic response. In the context of neutralizing antibodies to a biologic therapy, it can also be used as a functional measure activity of the drug. Presence of neutralizing antibodies to beta-interferons is known to inhibit response to therapy in patients with MS. Consequently, a Genesis® Comparative Analysis was performed using pre-Avonex treatment WBC samples as the reference set and post-Avonex treatment MS samples WBC samples as the experimental set. Parameters were as follows:

-   -   Log with Floor=0,     -   95% confidence level,     -   Unequal Variance,     -   Exclude expression with call values of “Unknown” or “No Value,”     -   MAS5.0 Affymetrix Summarization,     -   Include only gene fragments that do not have Affymetrix         “Present” Call in 100% of samples in either sample set,     -   Sample set expression lower and upper percentiles of 25 and 75,     -   Fold-change magnitude of +/−1.3,     -   Raw p-value threshold of 0.05.

This analysis yielded the set of 111 genes listed in Table 3. Gene expression values for the genes listed in Table 3 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

Further, many interferon-inducible genes were identified as markers for adequate treatment monitoring, and these include:

IFI44L interferon-induced protein 44-like RSAD2 radical S-adenosyl methionine domain containing 2 RSAD2 radical S-adenosyl methionine domain containing 2 IFI44 interferon-induced protein 44 MX1 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse LOC650557 similar to HLA class II histocompatibility antigen, DQ(W1.1) beta chain precursor IFIT3 interferon-induced protein with tetratricopeptide repeats 3 LY6E lymphocyte antigen 6 complex, locus E ISG15 ISG15 ubiquitin-like modifier BIRC4BP XIAP associated factor-1 LOC129607 hypothetical protein LOC129607 IFI44 interferon-induced protein 44 APOBEC3A apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A MS4A4A membrane-spanning 4-domains, subfamily A, member 4 IFIT2 interferon-induced protein with tetratricopeptide repeats 2 IFIT3 interferon-induced protein with tetratricopeptide repeats 3 PARP14 poly (ADP-ribose) polymerase family, member 14 IFI6 interferon, alpha-inducible protein 6

Example 3 Genes that are Differentially Expressed Between Pre- and Post-Copaxone Treatment MS Samples

Parameters were the same as for Example 2. This analysis yielded the set of 229 gene listed in Table 4. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33. Gene expression values for the genes listed in Table 4 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

Example 4 Genes that are Differentially Expressed Between Pre- and Post-Copaxone Treatment MS Samples and Between Pre- and Post-Avonex Treatment MS Samples

Avonex and Copaxone have distinct mechanisms of molecular action. Beta-interferon (Avonex) is a protein made by the body, thought primarily to combat viral infections. Glatiramer acetate (Copaxone) is a mixture of amino acids that bind to major histocompatibility complex class II molecules and competition with MBP and other myelin proteins for such binding and presentation to T cells. Genes that are altered in expression after treatment with both agents may represent a common signature of therapeutic benefit. Table 5 lists the genes that are common to both Table 3 and Table 4. Parameters were the same as for Example 2.

This analysis yielded the set of 36 gene fragments listed in Table 5. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

Gene expression values for the genes listed in Table 5 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

All patents or publications disclosed herein are incorporated by reference in their entireties.

TABLE 1A SEQ Genbank ID Bonferroni Stepup Mean Mean Gene Title Gene Symbol Acc. No. NO. p-value (p-value) (p-value) T (CONTROL) (MS) FK506 binding protein 5 FKBP5 NM_004117 0813 4.95E−20 2.71E−15 2.71E−15 −10.9889 78.0882 190.055 FK506 binding protein 5 FKBP5 W86302 1003 9.38E−18 5.13E−13 2.56E−13 −10.0535 473.34 934.916 FK506 binding protein 5 FKBP5 AI753747 0255 3.80E−17 2.08E−12 6.93E−13 −9.80302 1184.25 2126.26 cyclin D3 CCND3 NM_001760 0778 9.21E−13 5.04E−08 1.26E−08 −7.96208 2021.6 2569.7 tetraspanin 14 TSPAN14 NM_030927 0958 8.54E−12 4.67E−07 9.09E−08 −7.54226 436.935 543.259 chemokine (C—X—C motif) CXCR4 AF348491 0158 9.97E−12 5.45E−07 9.09E−08 −7.51268 1798.6 2290.67 receptor 4 Rho GTPase activating ARHGAP27 AI814329 0276 1.22E−11 6.65E−07 9.50E−08 −7.47481 47.2712 91.2659 protein 27 integrin, beta 2 ITGB2 L78790 0728 1.83E−11 1.00E−06 1.25E−07 −7.39644 3519.18 4443.09 (complement component 3 receptor 3 and 4 subunit) adrenergic, beta, receptor ADRBK1 M80776 0738 4.17E−11 2.28E−06 2.53E−07 −7.23859 275.479 414.407 kinase 1 solute carrier family 6 SLC6A6 NM_003043 0797 5.34E−11 2.92E−06 2.72E−07 −7.1906 125.121 202.558 (neurotransmitter transporter, taurine), member 6 Rho GTPase activating ARHGAP18 BE501862 0576 5.47E−11 2.99E−06 2.72E−07 7.18598 237.506 168.061 protein 18 DNA-damage-inducible DDIT4 NM_019058 0928 6.90E−11 3.77E−06 3.14E−07 −7.1411 247.135 427.375 transcript 4 chromodomain helicase CHD9 AW300405 0505 7.89E−11 4.31E−06 3.32E−07 7.11505 241.321 194.754 DNA binding protein 9 polypyrimidine tract PTBP1 AA679988 0041 9.27E−11 5.07E−06 3.54E−07 −7.08362 140.67 188.645 binding protein 1 DEAD (Asp-Glu-Ala-Asp) DDX6 NM_004397 0822 9.71E−11 5.31E−06 3.54E−07 7.07456 59.5517 43.1658 box polypeptide 6 transmembrane 9 TM9SF1 BE899402 0606 1.17E−10 6.40E−06 4.00E−07 −7.03808 95.4238 120.952 superfamily member 1 structural maintenance of SMC3 AI373676 0193 1.62E−10 8.88E−06 4.76E−07 6.97411 277.737 200.67 chromosomes 3 chromosome 6 open C6orf166 AI742378 0253 1.71E−10 9.35E−06 4.76E−07 −6.96395 84.0063 129.545 reading frame 166 salvador homolog 1 SAV1 AJ292969 0315 1.74E−10 9.52E−06 4.76E−07 6.96043 122.391 92.8185 (Drosophila) heat shock 70 kDa protein HSPA5 AF216292 0145 1.74E−10 9.52E−06 4.76E−07 −6.96042 1512.26 1749.33 5 (glucose-regulated protein, 78 kDa) MFNG O-fucosylpeptide MFNG AI738965 0249 2.02E−10 1.10E−05 5.26E−07 −6.93133 171.014 235.075 3-beta-N- acetylglucosaminyltransferase ankyrin repeat and BTB ABTB1 BF115480 0622 2.50E−10 1.37E−05 6.20E−07 −6.88974 39.5212 65.1926 (POZ) domain containing 1 leukotriene B4 receptor LTB4R U33448 0980 4.64E−10 2.54E−05 1.06E−06 −6.76716 127.687 245.457 myeloid cell leukemia MCL1 BF594446 0650 4.65E−10 2.54E−05 1.06E−06 −6.76677 182.812 295.014 sequence 1 (BCL2- related) Friend leukemia virus FLI1 M93255 0741 5.83E−10 3.19E−05 1.27E−06 −6.72202 620.183 755.664 integration 1 unc-93 homolog B1 UNC93B1 AW001274 0460 7.24E−10 3.96E−05 1.52E−06 −6.67888 130.118 217.625 (C. elegans) mindbomb homolog 1 MIB1 W80418 1001 8.62E−10 4.71E−05 1.71E−06 6.64405 230.686 181.53 (Drosophila) period homolog 1 PER1 NM_002616 0790 8.86E−10 4.85E−05 1.71E−06 −6.63854 54.7084 86.7084 (Drosophila) splicing factor, SFRS17A M99578 0743 9.08E−10 4.96E−05 1.71E−06 −6.63372 89.447 111.808 arginine/serine-rich 17A zinc finger and BTB ZBTB16 NM_006006 0849 9.49E−10 5.19E−05 1.73E−06 −6.62487 122.114 211.501 domain containing 16 ER lipid raft associated 1 ERLIN1 NM_006459 0862 9.95E−10 5.44E−05 1.76E−06 −6.61532 49.7838 68.0357 PHD finger protein 3 PHF3 AW189430 0482 1.05E−09 5.75E−05 1.80E−06 6.60417 170.33 132.083 toll-like receptor 2 TLR2 NM_003264 0801 1.15E−09 6.29E−05 1.85E−06 −6.58638 1897.07 2567.42 paxillin PXN D86862 0710 1.17E−09 6.39E−05 1.85E−06 −6.58298 92.9515 193.438 RAB GTPase activating RABGAP1L AB019490 0087 1.21E−09 6.62E−05 1.85E−06 6.57615 286.939 191.152 protein 1-like proline rich 14 PRR14 BE788667 0599 1.25E−09 6.82E−05 1.85E−06 −6.57015 122.602 235.313 Fc fragment of IgA, FCAR D87858 0712 1.25E−09 6.86E−05 1.85E−06 −6.56901 97.3093 155.905 receptor for tripeptidyl peptidase I TPP1 AA602532 0032 1.76E−09 9.62E−05 2.53E−06 −6.50075 200.439 264.395 signal-regulatory protein SIRPA D86043 0709 1.85E−09 0.000101 2.59E−06 −6.49062 69.319 119.932 alpha insulin-like growth factor 2 IGF2BP3 AU160004 0441 2.08E−09 0.000114 2.84E−06 6.46737 35.8267 21.3437 mRNA binding protein 3 RAN binding protein 3 RANBP3 AI689052 0244 2.52E−09 0.000138 3.36E−06 −6.42824 128.056 158.814 tankyrase, TRF1- TNKS2 BF060683 0615 2.84E−09 0.000155 3.69E−06 6.4041 346.06 256.529 interacting ankyrin-related ADP-ribose polymerase 2 transmembrane 9 TM9SF4 AI418892 0200 3.11E−09 0.00017 3.87E−06 −6.38564 167.867 208.305 superfamily protein member 4 CCR4-NOT transcription CNOT1 BC040523 0561 3.12E−09 0.00017 3.87E−06 −6.38501 70.5108 91.1365 complex, subunit 1 trophoblast-derived TncRNA AV659198 0443 3.26E−09 0.000178 3.93E−06 −6.37561 80.5859 112.859 noncoding RNA CD83 molecule CD83 NM_004233 0816 3.31E−09 0.000181 3.93E−06 6.37304 119.09 91.3124 Transcribed locus — AI032730 0160 3.49E−09 0.000191 4.05E−06 6.36222 195.488 149.453 TBC1 domain family, TBC1D2B BF195608 0625 3.90E−09 0.000213 4.23E−06 −6.33953 288.317 340.68 member 28 hypothetical protein FLJ10038 NM_017976 0918 3.91E−09 0.000214 4.23E−06 6.33873 86.1568 69.6291 FLJ10038 procollagen-proline, 2- P4HB AK075503 0362 3.93E−09 0.000215 4.23E−06 −6.33781 289.177 412.473 oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide Ewing sarcoma breakpoint EWSR1 /// AF327066 0156 3.95E−09 0.000216 4.23E−06 −6.3368 331.762 417.378 region 1 /// Friend FLI1 leukemia virus integration 1 Rab interacting lysosomal RILPL2 AI810244 0275 4.09E−09 0.000224 4.30E−06 −6.32963 726.676 871.377 protein-like 2 RAB5C, member RAS RAB5C AF141304 0136 4.41E−09 0.000241 4.54E−06 −6.31423 663.073 848.044 oncogene family SMAD specific E3 SMURF2 AY014180 0532 4.48E−09 0.000245 4.54E−06 6.31098 417.357 352.415 ubiquitin protein ligase 2 diacylglycerol lipase, beta DAGLB BE795104 0600 5.78E−09 0.000316 5.75E−06 −6.2587 76.1839 103.52 — — AW275093 0495 6.77E−09 0.00037 6.61E−06 6.22634 37.8503 25.7363 cisplatin resistance- CROP AW089673 0478 7.20E−09 0.000394 6.80E−06 6.21366 1253.96 1024.1 associated overexpressed protein CUG triplet repeat, RNA CUGBP2 AI652861 0231 7.22E−09 0.000395 6.80E−06 −6.21313 439.059 508.726 binding protein 2 cleft lip and palate CLPTM1 BC004865 0551 7.52E−09 0.000411 6.86E−06 −6.20462 269.664 340.303 associated transmembrane protein 1 plasminogen activator, PLAUR AY029180 0533 7.53E−09 0.000412 6.86E−06 −6.20442 407.032 590.904 urokinase receptor SH3 domain and SH3TC1 NM_018986 0926 7.68E−09 0.00042 6.89E−06 −6.20022 156.867 208.68 tetratricopeptide repeats 1 CCAAT/enhancer binding CEBPD AV655640 0442 7.96E−09 0.000435 7.02E−06 −6.19304 66.2588 101.6 protein (C/EBP), delta myotrophin MTPN AL533334 0410 8.33E−09 0.000455 7.23E−06 6.18357 2922.38 2651.39 diacylglycerol kinase, zeta DGKZ NM_003646 0806 8.88E−09 0.000486 7.50E−06 −6.17031 495.581 742.687 104 kDa coiled-coil domain CCDC95 AA743390 0052 9.01E−09 0.000492 7.50E−06 −6.16737 114.613 146.782 containing 95 golgi autoantigen, golgin GOLGA8B AI829170 0286 9.05E−09 0.000495 7.50E−06 6.16637 85.2551 49.0105 subfamily a, 8B O-linked N- OGT U77413 0990 9.95E−09 0.000544 8.02E−06 −6.14688 276.547 320.452 acetylglucosamine (GlcNAc) transferase (UDP-N- acetylgluco- samine:polypeptide-N- acetylglucosaminyl transferase) alpha thalassemia/mental ATRX /// AI650257 0227 1.01E−08 0.00055 8.02E−06 6.14467 408.475 331.005 retardation syndrome X- LOC728849 linked (RAD54 homolog, S. cerevisiae) /// similar to transcriptional regulator ATRX isoform 1 mitogen-activated protein MAP2K1 AI571419 0217 1.01E−08 0.000554 8.02E−06 −6.14319 404.667 463.791 kinase kinase 1 Glutathione S-transferase GSTK1 AV722006 0451 1.16E−08 0.000636 9.08E−06 6.11454 19.2432 11.7156 kappa 1 ATP-binding cassette, ABCC1 NM_004996 0833 1.27E−08 0.000694 9.77E−06 −6.09625 116.754 144.306 sub-family C (CFTR/MRP), member 1 chromosome 19 open C19orf6 AI805266 0270 1.32E−08 0.000719 9.99E−06 −6.0888 83.2411 131.22 reading frame 6 potassium channel KCTD5 AA872593 0073 1.34E−08 0.000732 1.00E−05 −6.08503 69.8096 86.2762 tetramerisation domain containing 5 Transcribed locus — AI767751 0265 1.60E−08 0.000873 1.18E−05 6.04842 71.4585 56.7931 leukotriene B4 receptor LTB4R U41070 0982 1.65E−08 0.0009 1.20E−05 −6.04214 138.048 192.488 TSC22 domain family, TSC22D3 NM_004089 0811 1.75E−08 0.000955 1.26E−05 −6.02976 544.464 834.605 member 3 peroxiredoxin 6 PRDX6 NM_004905 0831 1.78E−08 0.000971 1.26E−05 6.02632 877.551 731.524 6-phosphofructo-2- PFKFB2 AB044805 0093 1.86E−08 0.00102 1.30E−05 −6.01598 29.4293 42.6113 kinase/fructose-2,6- biphosphatase 2 chromobox homolog 4 (Pc CBX4 NM_003655 0807 1.88E−08 0.001028 1.30E−05 −6.01429 72.9469 113.789 class homolog, Drosophila) GTPase, IMAP family GIMAP5 AL080068 0378 1.99E−08 0.001088 1.36E−05 6.00246 95.8797 62.4753 member 5 surfeit 4 SURF4 AF078866 0123 2.03E−08 0.00111 1.37E−05 −5.99814 226.218 267.996 PHD finger protein 12 PHF12 AL161953 0399 2.12E−08 0.001158 1.41E−05 −5.98937 30.8623 52.3356 CCAAT/enhancer binding CEBPD NM_005195 0837 2.29E−08 0.001253 1.51E−05 −5.97285 2487.99 3256.48 protein (C/EBP), delta prion protein (p27-30) PRNP AV725328 0453 2.37E−08 0.001297 1.54E−05 −5.96555 110.316 135.332 (Creutzfeldt-Jakob disease, Gerstmann- Strausler-Scheinker syndrome, fatal familial insomnia) phosphoinositide-3- PIK3R5 NM_014308 0883 2.40E−08 0.001313 1.54E−05 −5.96298 182.242 221.794 kinase, regulatory subunit 5, p101 myotubularin related MTMR1 AK001816 0322 2.49E−08 0.001362 1.57E−05 −5.9552 65.8114 89.0136 protein 1 SLAIN motif family, SLAIN2 AI979301 0310 2.49E−08 0.001363 1.57E−05 5.95515 209.516 151.766 member 2 C-type lectin domain CLEC1B NM_016509 0902 2.90E−08 0.001584 1.80E−05 5.92338 93.1775 59.0062 family 1, member B tetratricopeptide repeat TTC7A BE205790 0568 3.05E−08 0.001666 1.87E−05 −5.91278 37.0092 50.8386 domain 7A suppressor of Ty 16 SUPT16H AK024072 0341 3.08E−08 0.001685 1.87E−05 5.91033 263.419 187.951 homolog (S. cerevisiae) SERPINE1 mRNA binding SERBP1 BC003049 0547 3.25E−08 0.001778 1.92E−05 5.89903 1399.78 1212.41 protein 1 RNA binding motif protein RBM14 AF315633 0153 3.26E−08 0.001782 1.92E−05 −5.89857 39.9955 59.7803 14 T-cell acute lymphocytic TAL1 NM_003189 0800 3.28E−08 0.001794 1.92E−05 5.89718 206.228 138.234 leukemia 1 Ras association RAPH1 AA194149 0014 3.30E−08 0.001805 1.92E−05 5.89586 48.0791 34.1444 (RAlGDS/AF-6) and pleckstrin homology domains 1 disabled homolog 2, DAB2 N21202 0744 3.55E−08 0.001939 2.01E−05 5.88069 97.375 73.5883 mitogen-responsive phosphoprotein (Drosophila) v-ets erythroblastosis virus ETS1 NM_005238 0840 3.55E−08 0.00194 2.01E−05 −5.8806 52.905 74.8306 E26 oncogene homolog 1 (avian) elastin microfibril EMILIN2 AL552384 0416 3.58E−08 0.001958 2.01E−05 −5.87865 39.6291 58.0146 interfacer 2 myosin IXB MYO9B NM_004145 0815 3.60E−08 0.001968 2.01E−05 −5.87757 63.7389 105.347 DnaJ (Hsp40) homolog, DNAJC13 BC043583 0562 3.70E−08 0.002021 2.04E−05 5.87194 25.7886 18.3726 subfamily C, member 13 acyl-Coenzyme A binding ACBD5 BC025309 0560 3.93E−08 0.002151 2.15E−05 5.85869 84.7927 62.1417 domain containing 5 Ras association RAPH1 AA194149 0014 4.25E−08 0.002321 2.30E−05 5.84254 31.6578 22.9448 (RAlGDS/AF-6) and pleckstrin homology domains 1 C-type lectin domain CLEC4E BC000715 0538 4.41E−08 0.002412 2.35E−05 −5.8344 829.005 1208.34 family 4, member E Fc fragment of IgA, FCAR U43677 0983 4.43E−08 0.002424 2.35E−05 −5.8333 63.8877 101.844 receptor for ATPase, Ca++ ATP2A3 AA877910 0076 4.84E−08 0.002649 2.52E−05 −5.81444 72.7871 103.656 transporting, ubiquitous methionine MAT2A NM_005911 0848 4.90E−08 0.002681 2.52E−05 −5.8119 97.8356 120.978 adenosyltransferase II, alpha general transcription factor GTF2A1 NM_015859 0891 4.94E−08 0.002701 2.52E−05 5.81025 49.1129 30.3493 IIA, 1, 19/37 kDa DAZ associated protein 2 DAZAP2 AL534321 0411 4.96E−08 0.002711 2.52E−05 −5.80949 1687.13 2024.25 chromosome 1 open C1orf38 AB035482 0091 4.98E−08 0.002723 2.52E−05 −5.80855 1388.6 1760.08 reading frame 38 arrestin domain containing 1 ARRDC1 AK001822 0323 5.37E−08 0.002936 2.69E−05 −5.79252 226.097 291.039 RAD23 homolog B RAD23B AL527365 0409 5.42E−08 0.002966 2.70E−05 −5.79036 500.181 673.845 (S. cerevisiae) chromosome 19 open C19orf6 AC004528 0097 5.59E−08 0.003057 2.75E−05 −5.78388 95.6151 147.154 reading frame 6 procollagen-proline, 2- P4HB J02783 0716 5.81E−08 0.003178 2.84E−05 −5.77559 1504.99 1750.23 oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide period homolog 1 PER1 AF022991 0108 6.03E−08 0.003298 2.92E−05 −5.76764 72.7414 94.1226 (Drosophila) galactosylceramidase GALC D25284 0705 6.24E−08 0.003413 2.99E−05 −5.76034 55.0178 65.2393 CDNA FLJ33748 fis, clone — H75391 0715 6.38E−08 0.00349 3.03E−05 5.75554 58.2421 42.1421 BRCAN2000148 glucosamine (N-acetyl)-6- GNS NM_002076 0782 6.49E−08 0.00355 3.06E−05 −5.75189 94.4501 134.182 sulfatase (Sanfilippo disease IIID) non-POU domain NONO L14599 0721 6.55E−08 0.00358 3.06E−05 −5.75007 523.202 604.536 containing, octamer- binding zinc finger protein 117 ZNF117 NM_024498 0946 6.86E−08 0.003749 3.18E−05 5.74018 140.903 101.407 activin A receptor, type IB ACVR1B AL117643 0384 7.04E−08 0.003851 3.24E−05 −5.73445 173.827 206.214 minichromosome MCM3AP AK022303 0333 7.15E−08 0.00391 3.26E−05 −5.73118 30.2496 41.9715 maintenance complex component 3 associated protein natural killer-tumor NKTR AA732581 0048 7.29E−08 0.003984 3.28E−05 5.72714 151.814 110.341 recognition sequence sorbin and SH3 domain SORBS3 MM_005775 0844 7.34E−08 0.004013 3.28E−05 −5.72558 27.3042 44.7622 containing 3 phosphoinositide-3-kinase PIK3IP1 BE042976 0563 7.42E−08 0.004058 3.28E−05 −5.7232 535.676 693.49 interacting protein 1 CDNA FLJ34061 fis, clone — BG430133 0695 7.44E−08 0.004065 3.28E−05 5.72283 40.264 27.4554 FCBBF3000462 heterogeneous nuclear HNRNPC AV725195 0452 8.11E−08 0.004435 3.53E−05 5.7041 1949.64 1687.13 ribonucleoprotein C (C1/C2) calnexin CANX AI761759 0258 8.14E−08 0.004453 3.53E−05 −5.70324 426.358 492.788 inositol polyphosphate-5- INPP5D U53470 0985 8.34E−08 0.004561 3.59E−05 −5.69807 246.284 314.816 phosphatase, 145 kDa hepatocellular carcinoma- HCRP1 AK025343 0356 8.40E−08 0.00459 3.59E−05 −5.69672 56.4645 71.8341 related HCRP1 solute carrier family 12 SLC12A9 BC000154 0535 9.12E−08 0.004986 3.83E−05 −5.6789 66.7681 99.8859 (potassium/chloride transporters), member 9 suppression of ST14 U20428 0979 9.16E−08 0.005011 3.83E−05 −5.67782 22.546 32.7603 tumorigenicity 14 (colon carcinoma) plasminogen activator, PLAUR U08839 0975 9.17E−08 0.005016 3.83E−05 −5.67761 524.092 709.03 urokinase receptor TAF8 RNA polymerase II, TAF8 BU618741 0703 9.40E−08 0.005138 3.89E−05 −5.67241 59.63 73.0919 TATA box binding protein (TBP)-associated factor, 43 kDa chemokine (C—X—C motif) CXCR4 L01639 0719 9.54E−08 0.005218 3.90E−05 −5.66907 1512.58 1818.68 receptor 4 N-acetylglucosamine-1- GNPTG AF302786 0151 9.56E−08 0.005226 3.90E−05 −5.66876 178.91 206.84 phosphate transferase, gamma subunit protein associated with PATL1 AA359612 0018 9.69E−08 0.005298 3.92E−05 −5.66579 72.1086 87.181 topoisomerase II homolog 1 (yeast) galactosidase, beta 1 GLB1 NM_000404 0758 1.04E−07 0.005679 4.18E−05 −5.6508 511.828 593.578 PDZ and LIM domain 2 PDLIM2 NM_021630 0934 1.05E−07 0.005739 4.19E−05 −5.64853 541.251 633.673 (mystique) (clone 1NIB-4) normalized — BQ002274 0702 1.08E−07 0.005882 4.26E−05 −5.64319 20.177 30.5449 cDNA library sequence transmembrane protein 43 TMEM43 W74580 1000 1.10E−07 0.006007 4.32E−05 −5.63862 440.535 521.401 exosome component 1 EXOSC1 BC012538 0559 1.11E−07 0.006085 4.35E−05 5.63584 38.3959 29.0411 transducin-like enhancer TLE4 AL358975 0400 1.15E−07 0.006276 4.45E−05 −5.62913 204.851 242.919 of split 4 (E(sp1) homolog, Drosophila) plectin 1, intermediate PLEC1 Z54367 1015 1.20E−07 0.006555 4.62E−05 −5.61971 95.9978 135.448 filament binding protein 500 kDa FIP1 like 1 (S. cerevisiae) FIP1L1 NM_030917 0957 1.23E−07 0.006726 4.70E−05 5.61413 201.771 180.087 blocked early in transport BET1L NM_016526 0903 1.25E−07 0.006853 4.74E−05 −5.61006 12.5373 29.2921 1 homolog (S. cerevisiae)- like SMEK homolog 1, SMEK1 NM_017936 0917 1.26E−07 0.006873 4.74E−05 5.60944 91.0002 70.0335 suppressor of mek1 (Dictyostelium) nuclear casein kinase and NUCKS1 AW515443 0516 1.28E−07 0.006977 4.78E−05 5.60618 1001.36 797.94 cyclin-dependent kinase substrate 1 myosin IXB MYO9B AF143684 0137 1.29E−07 0.007064 4.81E−05 −5.60349 301.367 426.587 zinc finger RNA binding ZFR AI459274 0207 1.33E−07 0.007252 4.90E−05 5.59779 90.3366 66.8956 protein chromosome 8 open C8orf42 AI632224 0222 1.35E−07 0.007362 4.94E−05 5.5945 19.8855 12.7616 reading frame 42 retinol saturase (all-trans- RETSAT AK098125 0364 1.35E−07 0.007405 4.94E−05 −5.59324 38.949 52.5054 retinol 13,14-reductase) protein kinase, AMP- PRKAB2 NM_005399 0841 1.50E−07 0.008186 5.39E−05 5.57142 44.2835 33.7496 activated, beta 2 non- catalytic subunit U2 small nuclear RNA U2AF2 NM_007279 0875 1.50E−07 0.008188 5.39E−05 −5.57136 111.086 152.14 auxiliary factor 2 WD repeat domain 1 WDR1 AF274954 0150 1.58E−07 0.008627 5.64E−05 −5.55997 413.045 580.746 PTK2 protein tyrosine PTK2 AL037339 0368 1.61E−07 0.008819 5.67E−05 5.55518 73.6126 59.6382 kinase 2 solute carrier family 16, SLC16A3 AL513917 0404 1.62E−07 0.008831 5.67E−05 −5.55488 372.042 569.693 member 3 (monocarboxylic acid transporter 4) tripartite motif-containing 8 TRIM8 NM_030912 0956 1.62E−07 0.008848 5.67E−05 5.55447 781.843 658.669 Full-length cDNA clone — AW953794 0525 1.74E−07 0.009534 6.05E−05 −5.53815 27.1676 38.0869 CS0DF032YA11 of Fetal brain of Homo sapiens (human) speckle-type POZ protein SPOP NM_003563 0805 1.75E−07 0.009565 6.05E−05 5.53745 917.406 826.599 BCL2-associated X BAX U19599 0977 1.77E−07 0.009659 6.07E−05 −5.53531 114.446 151.371 protein high mobility group AT- HMGA1 AF176039 0141 1.80E−07 0.009863 6.16E−05 −5.53073 22.5906 40.0994 hook 1 Transcribed locus — BE348304 0572 1.84E−07 0.010055 6.25E−05 5.52651 55.2633 42.0568 transmembrane and TMCO3 NM_017905 0914 1.89E−07 0.010358 6.39E−05 −5.52001 68.6431 86.2412 coiled-coil domains 3 C-type lectin domain CLEC4E NM_014358 0885 1.99E−07 0.010891 6.67E−05 −5.50901 152.544 201.687 family 4, member E chromosome 7 open C7orf27 AK024482 0345 2.00E−07 0.010939 6.67E−05 −5.50806 101.071 132.536 reading frame 27 suppressor of zeste 12 SUZ12 /// AI924660 0297 2.03E−07 0.011081 6.69E−05 5.50523 295.079 253.21 homolog (Drosophila) /// SUZ12P suppressor of zeste 12 homolog pseudogene unc-93 homolog B1 UNC93B1 NM_030930 0959 2.03E−07 0.011114 6.69E−05 −5.50458 89.4778 132.242 (C. elegans) Transcribed locus, — AI738675 0248 2.09E−07 0.011409 6.83E−05 −5.49882 394.226 504.553 strongly similar to XP_529518.1 PREDICTED: hypothetical protein XP_529518 [Pan troglodytes] differentially expressed in DEF6 NM_022047 0937 2.17E−07 0.011852 7.06E−05 −5.49046 287.062 338.604 FDCP 6 homolog (mouse) KIAA0146 KIAA0146 AI363213 0191 2.21E−07 0.01207 7.14E−05 −5.48646 80.4881 111.914 BCL6 co-repressor BCOR AF317392 0154 2.23E−07 0.012214 7.16E−05 5.48386 111.082 75.8345 KIAA0319-like KIAA0319L W58365 0999 2.24E−07 0.012251 7.16E−05 −5.48318 368.026 488.272 — — AK000677 0317 2.26E−07 0.012378 7.20E−05 5.48093 62.6473 48.142 ADP-dependent ADPGK BC006112 0557 2.32E−07 0.012687 7.33E−05 −5.47549 135.74 160.824 glucokinase TSC22 domain family, TSC22D3 AL110191 0382 2.34E−07 0.012819 7.37E−05 −5.47322 3412.5 4338.52 member 3 nemo-like kinase NLK NM_016231 0897 2.37E−07 0.012956 7.40E−05 5.47089 86.344 73.4371 amyloid beta (A4) APLP2 AW001847 0461 2.40E−07 0.013111 7.41E−05 −5.46827 677.954 884.114 precursor-like protein 2 phospholipase D family, PLD3 NM_012268 0878 2.41E−07 0.013179 7.41E−05 −5.46712 190.559 273.424 member 3 Transcribed locus — BF114745 0621 2.41E−07 0.01319 7.41E−05 5.46695 103.561 92.2368 ER lipid raft associated 1 ERLIN1 AL568449 0419 2.47E−07 0.013486 7.53E−05 −5.46206 340.054 398.739 Transcribed locus — H24473 0713 2.58E−07 0.014086 7.83E−05 5.45246 26.6195 19.7937 procollagen-proline, 2- P4HB NM_000918 0762 2.66E−07 0.014538 8.03E−05 −5.44549 795.05 902.135 oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide calreticulin CALR BE251303 0570 2.71E−07 0.014816 8.14E−05 −5.44132 356.88 465.235 PTK2B protein tyrosine PTK2B NM_004103 0812 2.73E−07 0.014902 8.14E−05 −5.44003 101.943 153.102 kinase 2 beta KIAA0892 KIAA0892 AC003030 0096 2.77E−07 0.01513 8.19E−05 −5.43668 15.0909 27.2329 angiotensin II receptor- AGTRAP AF165187 0139 2.77E−07 0.015159 8.19E−05 −5.43627 577.465 745.496 associated protein Transcribed locus — AW244016 0490 2.85E−07 0.015562 8.37E−05 −5.43047 108.711 161.89 Full length insert cDNA — AF086041 0124 2.90E−07 0.015846 8.40E−05 5.42647 73.6103 50.4274 clone YX53E08 suppression of ST14 NM_021978 0936 2.90E−07 0.015869 8.40E−05 −5.42615 36.3457 56.3781 tumorigenicity 14 (colon carcinoma) serologically defined colon SDCCAG1 BC006001 0556 2.92E−07 0.015938 8.40E−05 5.42519 413.226 349.695 cancer antigen 1 Cbp/p300-interacting CITED2 NM_006079 0852 2.92E−07 0.015952 8.40E−05 −5.425 256.843 305.525 transactivator, with Glu/Asp-rich carboxy- terminal domain, 2 ankyrin repeat and FYVE ANKFY1 NM_016376 0901 2.94E−07 0.016093 8.43E−05 −5.42305 86.1838 107.681 domain containing 1 interleukin 13 receptor, IL13RA1 NM_001560 0773 2.97E−07 0.016254 8.43E−05 −5.42085 640.164 787.654 alpha 1 EH domain binding protein EHBP1L1 AA149545 0012 2.98E−07 0.016276 8.43E−05 −5.42055 260.818 334.559 1-like 1 Rho GTPase activating ARHGAP4 NM_001666 0777 3.01E−07 0.016452 8.48E−05 −5.41817 204.777 266.516 protein 4 Transcribed locus — AW298731 0504 3.03E−07 0.016586 8.49E−05 −5.41638 27.4913 49.2688 Ras and Rab interactor 3 RIN3 AW027923 0470 3.07E−07 0.016787 8.49E−05 −5.4137 162.083 222.874 CDNA clone — N57510 0749 3.07E−07 0.016793 8.49E−05 5.41363 127.327 110.056 IMAGE: 5313062 Homo sapiens, clone — AV735241 0455 3.08E−07 0.016816 8.49E−05 5.41333 171.32 145.168 IMAGE: 3345917, mRNA pro-platelet basic protein PPBP R64130 0963 3.13E−07 0.017119 8.60E−05 5.40937 4143.9 2480.31 (chemokine (C—X—C motif) ligand 7) cell division cycle 2-like 1 CDC2L1 /// NM_001787 0779 3.18E−07 0.017373 8.69E−05 −5.40611 167.96 197.461 (PITSLRE proteins) /// cell CDC2L2 division cycle 2-like 2 (PITSLRE proteins) cysteine conjugate-beta CCBL2 BC000819 0540 3.28E−07 0.017938 8.92E−05 5.39902 322.023 274.341 lyase 2 sema domain, SEMA4A NM_022367 0939 3.36E−07 0.018372 9.09E−05 −5.39372 362.638 494.889 immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A Rho GDP dissociation ARHGDIA D13989 0704 3.41E−07 0.018624 9.14E−05 −5.3907 98.9323 215.826 inhibitor (GDI) alpha Wolf-Hirschhorn syndrome WHSC1L1 NM_017778 0912 3.41E−07 0.01864 9.14E−05 5.3905 68.4864 57.256 candidate 1-like 1 tissue factor pathway TFPI AF021834 0107 3.46E−07 0.018898 9.22E−05 5.38745 21.9809 12.7738 inhibitor (lipoprotein- associated coagulation inhibitor) zinc finger protein 271 ZNF271 AF159567 0138 3.56E−07 0.019471 9.43E−05 5.38082 179.018 149.631 Wiskott-Aldrich syndrome WAS NM_000377 0757 3.57E−07 0.019512 9.43E−05 −5.38036 184.107 410.974 (eczema- thrombocytopenia) EH domain binding protein 1 EHBP1 BF116032 0624 3.63E−07 0.019842 9.54E−05 5.37662 96.9949 68.9836 solute carrier family 6 SLC6A6 U16120 0976 3.71E−07 0.020295 9.65E−05 −5.37161 60.7858 85.2317 (neurotransmitter transporter, taurine), member 6 ADAM metallopeptidase ADAM8 AI814527 0277 3.72E−07 0.020315 9.65E−05 −5.37139 120.008 221.72 domain 8 zinc finger protein 36, C3H ZFP36L2 AI356398 0189 3.73E−07 0.020368 9.65E−05 −5.37081 563.157 986.407 type-like 2 RAB27B, member RAS RAB27B BF438386 0637 3.77E−07 0.020613 9.72E−05 5.36815 187.305 137.411 oncogene family versican VCAN D32039 0706 3.79E−07 0.020739 9.74E−05 −5.36679 1066.01 1372.33 Interleukin 8 IL8 AJ239383 0313 4.33E−07 0.02365 0.000108 −5.33753 75.0461 119.62 leukocyte immunoglobulin- LILRA2 U82277 0993 4.81E−07 0.026298 0.000116 −5.31382 349.215 498.426 like receptor, subfamily A (with TM domain), member 2 immunoglobulin heavy IGH@ /// S55735 0965 5.11E−07 0.027913 0.000122 −5.30048 2641.16 4723.74 locus /// immunoglobulin IGHA1 /// heavy constant alpha 1 /// IGHA2 /// immunoglobulin heavy LOC100126583 constant alpha 2 (A2m marker) /// hypothetical LOC100126583 regulator of G-protein RGS14 AF037194 0109 5.12E−07 0.027979 0.000122 −5.29995 80.6164 117.832 signaling 14 F-box protein 9 FBXO9 AK095315 0363 5.15E−07 0.028176 0.000122 5.29838 1081.96 798.526 septin 9 9-Sep NM_006640 0865 5.17E−07 0.028263 0.000122 −5.29769 87.4231 164.873 myeloid cell leukemia MCL1 NM_021960 0935 5.40E−07 0.029511 0.000126 −5.288 3409.06 4155.72 sequence 1 (BCL2- related) poly(A) polymerase alpha PAPOLA BF797555 0662 5.74E−07 0.031378 0.00013 5.27423 1470.85 1208.87 Transcribed locus — AI492388 0212 6.97E−07 0.038094 0.00015 −5.23055 216.947 349.917 Rho GDP dissociation ARHGDIA AI571798 0218 7.40E−07 0.040446 0.000155 −5.21702 94.6544 217.268 inhibitor (GDI) alpha guanine nucleotide GNAZ NM_002073 0781 7.49E−07 0.040958 0.000155 5.21417 138.429 84.1772 binding protein (G protein), alpha z polypeptide ATPase, Ca++ ATP2A3 AF068220 0120 8.34E−07 0.04561 0.000168 −5.18981 95.5902 142.894 transporting, ubiquitous prostaglandin- PTGS1 BE613133 0580 9.28E−07 0.050719 0.000182 5.1657 276.922 176.715 endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) ankyrin repeat and BTB ABTB1 AW511257 0514 9.52E−07 0.052074 0.000185 −5.15971 39.4124 61.2487 (POZ) domain containing 1 folate receptor 1 (adult) FOLR1 AF000381 0102 1.38E−06 0.075578 0.000238 5.07454 1958.77 1397.2 Fc fragment of IgA, FCAR NM_002000 0780 1.45E−06 0.079201 0.000246 −5.06377 177.357 246.89 receptor for G-protein signaling GPSM3 BG111168 0671 1.76E−06 0.095967 0.00028 −5.01948 477.969 796.568 modulator 3 (AGS3-like, C. elegans) Spermatid perinuclear STRBP AK024960 0353 1.93E−06 0.105266 0.000299 4.99807 44.2908 29.796 RNA binding protein enoyl Coenzyme A ECHDC3 NM_024693 0948 2.10E−06 0.114859 0.000316 −4.97782 61.4091 98.8895 hydratase domain containing 3 heterogeneous nuclear HNRNPC NM_004500 0824 2.17E−06 0.118742 0.000322 4.97009 1575.25 1401.51 ribonucleoprotein C (C1/C2) colony stimulating factor 3 CSF3R NM_000760 0761 2.36E−06 0.128959 0.000344 −4.95087 3038.28 4004.48 receptor (granulocyte) myosin, light chain 6, MYL6 BE734356 0594 2.45E−06 0.134031 0.000356 4.94187 5732.33 4706.58 alkali, smooth muscle and non-muscle strawberry notch homolog SBNO2 AC005390 0100 2.72E−06 0.148716 0.000383 −4.91756 126.198 194.376 2 (Drosophila) DEAD (Asp-Glu-Ala-Asp) DDX17 AA521056 0025 2.79E−06 0.152295 0.000387 4.91199 3247.14 2585.45 box polypeptide 17 amyotrophic lateral ALS2CR12 AI057333 0163 3.30E−06 0.180188 0.000423 4.8725 92.0138 46.3901 sclerosis 2 (juvenile) chromosome region, candidate 12 egl nine homolog 2 EGLN2 AW057545 0472 3.41E−06 0.186485 0.000434 −4.8644 46.7042 81.0448 (C. elegans) WD and tetratricopeptide WDTC1 AK001734 0321 3.74E−06 0.204421 0.000464 −4.84273 143.089 215.035 repeats 1 CD74 molecule, major CD74 M28590 0733 3.99E−06 0.218102 0.000477 −4.82741 393.178 654.678 histocompatibility complex, class II invariant chain glycoprotein VI (platelet) GP6 AB043821 0092 4.78E−06 0.261363 0.000537 4.78445 95.1473 61.4523 dual specificity DUSP1 AA530892 0027 4.79E−06 0.261693 0.000537 −4.78415 107.394 209.5 phosphatase 1 transcription factor binding TFE3 AY034078 0534 4.79E−06 0.262114 0.000537 −4.78376 58.8061 97.4688 to IGHM enhancer 3 gelsolin (amyloidosis, GSN BE675337 0587 4.83E−06 0.2639 0.000538 −4.78215 77.2986 118.847 Finnish type) guanine nucleotide GNG11 NM_004126 0814 4.83E−06 0.264071 0.000538 4.78199 548.288 339.78 binding protein (G protein), gamma 11 CD6 molecule CD6 NM_006725 0867 5.60E−06 0.306414 0.000594 −4.74649 92.2557 150.98 nerve growth factor NGFRAP1 NM_014380 0886 6.87E−06 0.375513 0.000699 4.69768 691.606 498.72 receptor (TNFRSF16) associated protein 1 selectin P ligand SELPLG AI741056 0250 7.68E−06 0.419967 0.000755 −4.67069 2721.41 3268.22 CD44 molecule (Indian CD44 AF098641 0127 7.70E−06 0.420973 0.000756 −4.67012 371.069 433.064 blood group) ORAI calcium release- ORAI2 BF939788 0663 7.87E−06 0.430403 0.000771 −4.66476 59.2229 93.4356 activated calcium modulator 2 prosaposin (variant PSAP M32221 0734 8.14E−06 0.444966 0.000787 −4.65671 5511.12 6507.81 Gaucher disease and variant metachromatic leukodystrophy) cortactin CTTN NM_005231 0839 8.54E−06 0.467172 0.000808 4.64491 182.112 121.169 CD6 molecule CD6 U66145 0988 9.03E−06 0.493658 0.00084 −4.63152 108.146 166.093 potassium voltage-gated KCNAB2 AF044253 0112 9.05E−06 0.494828 0.00084 −4.63095 32.1399 55.8352 channel, shaker-related subfamily, beta member 2 tyrosine 3- YWHAZ NM_003406 0803 1.07E−05 0.585411 0.000955 4.58999 3462.95 2974.74 monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide prefoldin subunit 5 PFDN5 NM_002624 0793 1.11E−05 0.608358 0.000981 4.58059 1086.43 759.973 zinc finger E-box binding ZEB2 AV739670 0456 1.26E−05 0.687237 0.00107 4.5507 90.1064 58.9124 homeobox 2 lymphocyte-specific LSP1 NM_002339 0784 1.80E−05 0.983838 0.001356 −4.46201 2289.02 2996.22 protein 1 GM2 ganglioside activator GM2A AL513583 0403 1.94E−05 1 0.001433 −4.44336 295.155 407.539 B-cell CLL/lymphoma 3 BCL3 AI829875 0287 2.01E−05 1 0.001474 −4.43457 73.2591 122.329 signal-regulatory protein SIRPA AC004832 0099 2.15E−05 1 0.00155 −4.41809 66.2175 114.978 alpha chromosome 21 open C21orf7 NM_020152 0932 2.42E−05 1 0.00169 4.3876 280.123 180.541 reading frame 7 arachidonate 12- ALOX12 NM_000697 0760 2.59E−05 1 0.001773 4.37069 142.898 92.6631 lipoxygenase immunoglobulin heavy IGHD AJ275469 0314 2.75E−05 1 0.001841 −4.35534 115.496 181.147 constant delta signal-regulatory protein SIRPA NM_004648 0827 2.87E−05 1 0.001899 −4.34524 277.486 340.134 alpha talin 1 TLN1 NM_006289 0857 3.03E−05 1 0.001968 −4.33118 677.305 962.298 versican VCAN R94644 0964 3.18E−05 1 0.002032 −4.31901 1312.01 1597.22 leukocyte immunoglobulin- LILRA4 AF041261 0110 3.36E−05 1 0.002112 −4.30455 50.1417 71.7018 like receptor, subfamily A (with TM domain), member 4 dual specificity DUSP1 NM_004417 0823 3.50E−05 1 0.002177 −4.2941 2510.99 3381.13 phosphatase 1 leukocyte immunoglobulin- LILRA2 U82278 0994 3.51E−05 1 0.002177 −4.29389 1033.51 1293.64 like receptor, subfamily A (with TM domain), member 2 leukocyte immunoglobulin- LILRA2 U82276 0992 3.94E−05 1 0.002317 −4.26416 899.494 1137.99 like receptor, subfamily A (with TM domain), member 2 colony stimulating factor 3 CSF3R NM_172313 0960 4.66E−05 1 0.002581 −4.22109 3895.82 4816.3 receptor (granulocyte) immunoglobulin lambda IGL@ D87021 0711 4.82E−05 1 0.002642 −4.21222 44.8257 78.8501 locus opioid growth factor OGFR AF172449 0140 5.54E−05 1 0.002911 −4.17619 54.9759 81.4231 receptor BCL2-associated BAG1 NM_004323 0820 5.83E−05 1 0.003012 4.16308 3331.77 2495.07 athanogene tetraspanin 5 TSPAN5 AF065389 0119 6.55E−05 1 0.003253 4.13256 1141.55 805.081 platelet factor 4 PF4 NM_002619 0791 7.11E−05 1 0.003433 4.11123 2982.12 2052.36 (chemokine (C—X—C motif) ligand 4) Fc fragment of IgA, FCAR U56237 0986 7.24E−05 1 0.003466 −4.10642 22.6711 32.7601 receptor for transketolase (Wernicke- TKT BF696840 0656 7.66E−05 1 0.003582 −4.09169 2569.82 3111.72 Korsakoff syndrome) heterogeneous nuclear HNRNPC AA664258 0039 8.17E−05 1 0.003762 4.07462 1778.78 1539.09 ribonucleoprotein C (C1/C2) tumor necrosis factor TNFRSF10C NM_003841 0808 8.60E−05 1 0.003866 −4.06101 1233.42 1735.81 receptor superfamily, member 10c, decoy without an intracellular domain clusterin CLU M25915 0732 0.000109 1 0.00464 3.99777 917.982 586.775 Interleukin 8 IL8 L34164 0723 0.000115 1 0.004824 −3.98299 68.9562 113.762 chromosome Y open CYorf15A AW468885 0510 0.000124 1 0.005062 3.96438 61.848 33.1275 reading frame 15A insulin-like growth factor 1 IGF1R BF347362 0633 0.000127 1 0.005152 −3.95765 22.2597 31.1978 receptor Immunoglobulin heavy IGHG1 M24668 0731 0.000144 1 0.005654 −3.92265 42.8722 66.9195 constant gamma 1 (G1m marker) adducin 3 (gamma) ADD3 AI763123 0262 0.000155 1 0.005926 3.90373 2119.65 1920.44 GM2 ganglioside activator GM2A M76477 0737 0.000176 1 0.006491 −3.86822 21.724 39.5498 small EDRK-rich factor 2 SERF2 BE568651 0579 0.000179 1 0.00656 3.86335 4954.6 4192.08 neurofilament, light NEFL AL537457 0413 0.000179 1 0.006562 3.86307 31.9431 23.1309 polypeptide 68 kDa hypothetical protein LOC284701 AL137733 0398 0.000218 1 0.007625 −3.80903 64.9496 112.816 LOC284701 interferon regulatory factor 7 IRF7 NM_004030 0810 0.000231 1 0.007884 −3.79395 409.493 623.352 CTD (carboxy-terminal CTDSPL NM_005808 0846 0.000235 1 0.00799 3.78905 93.671 62.2121 domain, RNA polymerase II, polypeptide A) small phosphatase-like immunoglobulin heavy IGHA1 /// U92706 0997 0.000252 1 0.008417 −3.76895 86.7125 132.558 constant alpha 1 /// IGHG1 /// immunoglobulin heavy IGHG3 /// constant gamma 1 (G1m IGHM /// marker) /// immunoglobulin IGHV4-31 heavy constant gamma 3 (G3m marker) /// immunoglobulin heavy constant mu /// immunoglobulin heavy variable 4-31 calreticulin CALR NM_004343 0821 0.00026 1 0.008592 −3.76047 79.4426 119.207 profilin 1 PFN1 NM_005022 0834 0.000262 1 0.008638 −3.75833 6953.19 7641.43 GM2 ganglioside activator GM2A M76477 0737 0.000299 1 0.009457 −3.72107 162.01 213.128 Immunoglobulin heavy IGHA1 AW519168 0517 0.000324 1 0.009983 −3.69913 152.921 219.57 constant alpha 1 BCL2-associated BAG1 AF116273 0132 0.000352 1 0.010602 3.67548 3286.14 2540.18 athanogene integrin, beta 2 ITGB2 NM_000211 0756 0.000355 1 0.010648 −3.67283 5760.57 6367.25 (complement component 3 receptor 3 and 4 subunit) integral membrane protein ITM2B AF092128 0126 0.000477 1 0.013182 −3.58869 10431.6 11336.4 2B myeloid cell leukemia MCL1 AI275690 0180 0.000503 1 0.013715 −3.5734 6463.22 7020.98 sequence 1 (BCL2- related) GNAS complex locus GNAS AA650558 0038 0.000515 1 0.013953 3.56649 1501.58 1173 tubulin, beta 1 TUBB1 N63244 0750 0.000816 1 0.019091 3.4314 2271.09 1745.37 ribosomal protein L23 RPL23 NM_000978 0767 0.000818 1 0.019126 3.43065 2085.23 1502.85 peroxiredoxin 6 PRDX6 BE869583 0604 0.000914 1 0.020772 3.39769 3442.93 2661.75 neurofilament, light NEFL BF055311 0613 0.00094 1 0.021238 3.38918 82.1 61.5983 polypeptide 68 kDa immunoglobulin kappa IGK@ /// IGKC AW575927 0518 0.001341 1 0.027148 −3.28165 4837.67 5839.72 constant /// /// IGKV1-5 /// immunoglobulin kappa IGKV2-24 variable 1-5 /// immunoglobulin kappa variable 2-24 /// immunoglobulin kappa locus cystatin C (amyloid CST3 NM_000099 0755 0.001346 1 0.027219 −3.28039 3566.07 4248.09 angiopathy and cerebral hemorrhage) ribosomal protein L7 RPL7 NM_000971 0766 0.001461 1 0.028666 3.25511 6070.42 4837.24 interferon induced IFITM1 AA749101 0057 0.001797 1 0.033003 −3.19088 7152.48 8178.72 transmembrane protein 1 (9-27) ribosomal protein L36a /// LOC729362 /// NM_021029 0933 0.001813 1 0.03322 3.18807 4537.53 3218.25 similar to large subunit RPL36A ribosomal protein L36a SUB1 homolog (S. cerevisiae) SUB1 BE784583 0598 0.001896 1 0.034265 3.17412 1392.33 1081.88 guanylate kinase 1 GUK1 BC006249 0558 0.001983 1 0.035305 3.15989 4000.02 3171.59 Pre-B-cell colony PBEF1 AA873350 0074 0.002161 1 0.037276 −3.13274 3292.91 3867.52 enhancing factor 1 prostaglandin- PTGS1 NM_000962 0764 0.002218 1 0.037809 3.12446 103.535 79.4279 endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) F-box protein 7 FBXO7 NM_012179 0877 0.002317 1 0.038996 3.11068 6069.43 5014.48 hemoglobin, alpha 1 /// HBA1 /// HBA2 AF105974 0128 0.002367 1 0.039561 3.10384 6124.77 4656.14 hemoglobin, alpha 2 hemoglobin, alpha 1 HBA1 BC005931 0555 0.00239 1 0.039846 3.10074 6143.06 4645.89 immunoglobulin lambda IGL@ /// IGLJ3 X57812 1008 0.002707 1 0.043327 −3.06075 3476.47 4451 locus /// immunoglobulin /// IGLV2-14 /// lambda variable 4-3 /// IGLV3-25 /// immunoglobulin lambda IGLV4-3 variable 3-25 /// immunoglobulin lambda variable 2-14 /// immunoglobulin lambda joining 3 major histocompatibility HLA-G M90686 0740 0.002992 1 0.046215 −3.02834 5755.57 7193.31 complex, class I, G SUB1 homolog (S. cerevisiae) SUB1 BG231551 0678 0.003023 1 0.046448 3.02497 2004.47 1599.13 chemokine (C—X3—C motif) CX3CR1 U20350 0978 0.003112 1 0.04726 3.0156 2713.44 2373.65 receptor 1 metastasis associated MALAT1 AF132202 0134 0.003436 1 0.050486 −2.98318 6262.75 7016.01 lung adenocarcinoma transcript 1 (non-protein coding) metastasis associated MALAT1 BG534952 0699 0.00728 1 0.08193 2.72885 6776.17 6030.81 lung adenocarcinoma transcript 1 (non-protein coding) tubulin, beta 2A TUBB2A NM_001069 0768 0.017717 1 0.144043 2.40355 1238.52 689.685 solute carrier family 25, SLC25A37 BG251467 0679 0.019789 1 0.154414 2.36091 7684.14 6998.66 member 37 solute carrier family 25, SLC25A37 BG251467 0679 0.037867 1 0.228447 2.09875 4732.41 4047.49 member 37 GNAS complex locus GNAS NM_016592 0905 0.060396 1 0.298237 1.89518 6053.88 5672.78 metastasis associated MALAT1 BE708432 0592 0.097547 1 0.387215 1.66947 15502.2 14795.3 lung adenocarcinoma transcript 1 (non-protein coding)

TABLE 1B MeanDiff Genbank SEQ ID MeanRatio (CONTROL − FoldChange Gene Title Gene Symbol Acc. No. NO. (CONTROL/MS) MS) (CONTROL/MS) Probe Set ID FK506 binding protein 5 FKBP5 NM_004117 0813 0.410872 −111.966 −2.43385 204560_at FK506 binding protein 5 FKBP5 W86302 1003 0.506291 −461.576 −1.97515 224856_at FK506 binding protein 5 FKBP5 AI753747 0255 0.556963 −942.013 −1.79545 224840_at cyclin D3 CCND3 NM_001760 0778 0.786706 −548.102 −1.27112 201700_at tetraspanin 14 TSPAN14 NM_030927 0958 0.804285 −106.324 −1.24334 221002_s_at chemokine (C—X—C motif) CXCR4 AF348491 0158 0.785186 −492.069 −1.27358 211919_s_at receptor 4 Rho GTPase activating ARHGAP27 AI814329 0276 0.51795 −43.9948 −1.93069 227057_at protein 27 integrin, beta 2 ITGB2 L78790 0728 0.792057 −923.911 −1.26254 1555349_a_at (complement component 3 receptor 3 and 4 subunit) adrenergic, beta, receptor ADRBK1 M80776 0738 0.664754 −138.928 −1.50432 201401_s_at kinase 1 solute carrier family 6 SLC6A6 NM_003043 0797 0.617703 −77.4371 −1.6189 205920_at (neurotransmitter transporter, taurine), member 6 Rho GTPase activating ARHGAP18 BE501862 0576 1.41321 69.4447 1.41321 225173_at protein 18 DNA-damage-inducible DDIT4 NM_019058 0928 0.578263 −180.24 −1.72932 202887_s_at transcript 4 chromodomain helicase CHD9 AW300405 0505 1.23911 46.5668 1.23911 229586_at DNA binding protein 9 polypyrimidine tract PTBP1 AA679988 0041 0.745687 −47.9749 −1.34105 212016_s_at binding protein 1 DEAD (Asp-Glu-Ala-Asp) DDX6 NM_004397 0822 1.3796 16.3859 1.3796 204909_at box polypeptide 6 transmembrane 9 TM9SF1 BE899402 0606 0.788937 −25.5286 −1.26753 209149_s_at superfamily member 1 structural maintenance of SMC3 AI373676 0193 1.38405 77.0678 1.38405 209258_s_at chromosomes 3 chromosome 6 open C6orf166 AI742378 0253 0.64847 −45.5391 −1.54209 223143_s_at reading frame 166 salvador homolog 1 SAV1 AJ292969 0315 1.3186 29.5723 1.3186 234491_s_at (Drosophila) heat shock 70 kDa protein HSPA5 AF216292 0145 0.864477 −237.075 −1.15677 211936_at 5 (glucose-regulated protein, 78 kDa) MFNG O-fucosylpeptide MFNG AI738965 0249 0.727485 −64.0613 −1.3746 204152_s_at 3-beta-N- acetylglucosaminyltransferase ankyrin repeat and BTB ABTB1 BF115480 0622 0.606222 −25.6714 −1.64956 242567_at (POZ) domain containing 1 leukotriene B4 receptor LTB4R U33448 0980 0.520201 −117.77 −1.92234 216388_s_at myeloid cell leukemia MCL1 BF594446 0650 0.619672 −112.202 −1.61376 200796_s_at sequence 1 (BCL2- related) Friend leukemia virus FLI1 M93255 0741 0.820712 −135.481 −1.21845 210786_s_at integration 1 unc-93 homolog B1 (C. elegans) UNC93B1 AW001274 0460 0.597899 −87.5072 −1.67252 225869_s_at mindbomb homolog 1 MIB1 W80418 1001 1.27079 49.1563 1.27079 224726_at (Drosophila) period homolog 1 PER1 NM_002616 0790 0.630947 −32 −1.58492 202861_at (Drosophila) splicing factor, SFRS17A M99578 0743 0.800003 −22.3614 −1.25 210269_s_at arginine/serine-rich 17A zinc finger and BTB ZBTB16 NM_006006 0849 0.577369 −89.3868 −1.73199 205883_at domain containing 16 ER lipid raft associated 1 ERLIN1 NM_006459 0862 0.73173 −18.2519 −1.36662 202444_s_at PHD finger protein 3 PHF3 AW189430 0482 1.28957 38.2468 1.28957 217951_s_at toll-like receptor 2 TLR2 NM_003264 0801 0.738901 −670.351 −1.35336 204924_at paxillin PXN D86862 0710 0.480522 −100.487 −2.08107 211823_s_at RAB GTPase activating RABGAP1L AB019490 0087 1.5011 95.7868 1.5011 215342_s_at protein 1-like proline rich 14 PRR14 BE788667 0599 0.521016 −112.711 −1.91933 1559397_s_at Fc fragment of IgA, FCAR D87858 0712 0.62416 −58.5952 −1.60215 211816_x_at receptor for tripeptidyl peptidase I TPP1 AA602532 0032 0.758102 −63.9567 −1.31908 214196_s_at signal-regulatory protein SIRPA D86043 0709 0.577984 −50.6133 −1.73015 202895_s_at alpha insulin-like growth factor 2 IGF2BP3 AU160004 0441 1.67856 14.483 1.67856 203819_s_at mRNA binding protein 3 RAN binding protein 3 RANBP3 AI689052 0244 0.806327 −30.7581 −1.24019 202639_s_at tankyrase, TRF1- TNKS2 BF060683 0615 1.34901 89.5309 1.34901 222562_s_at interacting ankyrin-related ADP-ribose polymerase 2 transmembrane 9 TM9SF4 AI418892 0200 0.805871 −40.4381 −1.24089 212194_s_at superfamily protein member 4 CCR4-NOT transcription CNOT1 BC040523 0561 0.773683 −20.6257 −1.29252 1554052_at complex, subunit 1 trophoblast-derived TncRNA AV659198 0443 0.714038 −32.2735 −1.40049 238320_at noncoding RNA CD83 molecule CD83 NM_004233 0816 1.30421 27.778 1.30421 204440_at Transcribed locus — AI032730 0160 1.30802 46.0351 1.30802 244679_at TBC1 domain family, TBC1D2B BF195608 0625 0.846298 −52.3633 −1.18162 212796_s_at member 2B hypothetical protein FLJ10038 NM_017976 0918 1.23737 16.5277 1.23737 205511_at FLJ10038 procollagen-proline, 2- P4HB AK075503 0362 0.70108 −123.296 −1.42637 1564494_s_at oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide Ewing sarcoma breakpoint EWSR1 /// AF327066 0156 0.794872 −85.6159 −1.25806 211825_s_at region 1 /// Friend FLI1 leukemia virus integration 1 Rab interacting lysosomal RILPL2 AI810244 0275 0.833939 −144.701 −1.19913 227983_at protein-like 2 RAB5C, member RAS RAB5C AF141304 0136 0.781885 −184.971 −1.27896 201156_s_at oncogene family SMAD specific E3 SMURF2 AY014180 0532 1.18427 64.941 1.18427 205596_s_at ubiquitin protein ligase 2 diacylglycerol lipase, beta DAGLB BE795104 0600 0.735937 −27.3357 −1.35881 225833_at — — AW275093 0495 1.4707 12.114 1.4707 242929_at cisplatin resistance- CROP AW089673 0478 1.22445 229.86 1.22445 208835_s_at associated overexpressed protein CUG triplet repeat, RNA CUGBP2 AI652861 0231 0.863056 −69.6671 −1.15867 227178_at binding protein 2 cleft lip and palate CLPTM1 BC004865 0551 0.792422 −70.6394 −1.26195 211136_s_at associated transmembrane protein 1 plasminogen activator, PLAUR AY029180 0533 0.688829 −183.872 −1.45174 211924_s_at urokinase receptor SH3 domain and SH3TC1 NM_018986 0926 0.751709 −51.8135 −1.3303 219256_s_at tetratricopeptide repeats 1 CCAAT/enhancer binding CEBPD AV655640 0442 0.652156 −35.3408 −1.53337 213006_at protein (C/EBP), delta myotrophin MTPN AL533334 0410 1.10221 270.99 1.10221 224656_s_at diacylglycerol kinase, zeta DGKZ NM_003646 0806 0.667281 −247.106 −1.49862 207556_s_at 104 kDa coiled-coil domain CCDC95 AA743390 0052 0.780837 −32.1692 −1.28068 227286_at containing 95 golgi autoantigen, golgin GOLGA8B AI829170 0286 1.73953 36.2445 1.73953 208797_s_at subfamily a, 8B O-linked N- OGT U77413 0990 0.86299 −43.9052 −1.15876 207563_s_at acetylglucosamine (GlcNAc) transferase (UDP-N- acetylglucosamine:polypeptide- N- acetylglucosaminyl transferase) alpha thalassemia/mental ATRX /// AI650257 0227 1.23404 77.4692 1.23404 208859_s_at retardation syndrome X- LOC728849 linked (RAD54 homolog, S. cerevisiae) /// similar to transcriptional regulator ATRX isoform 1 mitogen-activated protein MAP2K1 AI571419 0217 0.87252 −59.124 −1.14611 202670_at kinase kinase 1 Glutathione S-transferase GSTK1 AV722006 0451 1.64253 7.52765 1.64253 243325_at kappa 1 ATP-binding cassette, ABCC1 NM_004996 0833 0.809071 −27.5522 −1.23599 202805_s_at sub-family C (CFTR/MRP), member 1 chromosome 19 open C19orf6 AI805266 0270 0.634364 −47.9788 −1.57638 213986_s_at reading frame 6 potassium channel KCTD5 AA872593 0073 0.809141 −16.4666 −1.23588 222645_s_at tetramerisation domain containing 5 Transcribed locus — AI767751 0265 1.25823 14.6655 1.25823 228084_at leukotriene B4 receptor LTB4R U41070 0982 0.717178 −54.4399 −1.39435 210128_s_at TSC22 domain family, TSC22D3 NM_004089 0811 0.652362 −290.14 −1.53289 207001_x_at member 3 peroxiredoxin 6 PRDX6 NM_004905 0831 1.19962 146.027 1.19962 200845_s_at 6-phosphofructo-2- PFKFB2 AB044805 0093 0.690646 −13.182 −1.44792 209992_at kinase/fructose-2,6- biphosphatase 2 chromobox homolog 4 (Pc CBX4 NM_003655 0807 0.641073 −40.8418 −1.55988 206724_at class homolog, Drosophila) GTPase, IMAP family GIMAP5 AL080068 0378 1.53468 33.4044 1.53468 215352_at member 5 surfeit 4 SURF4 AF078866 0123 0.84411 −41.7779 −1.18468 222979_s_at PHD finger protein 12 PHF12 AL161953 0399 0.5897 −21.4733 −1.69578 234939_s_at CCAAT/enhancer binding CEBPD NM_005195 0837 0.764013 −768.486 −1.30888 203973_s_at protein (C/EBP), delta prion protein (p27-30) PRNP AV725328 0453 0.815149 −25.0163 −1.22677 215707_s_at (Creutzfeldt-Jakob disease, Gerstmann- Strausler-Scheinker syndrome, fatal familial insomnia) phosphoinositide-3- PIK3R5 NM_014308 0883 0.821673 −39.5518 −1.21703 220566_at kinase, regulatory subunit 5, p101 myotubularin related MTMR1 AK001816 0322 0.739341 −23.2022 −1.35256 214975_s_at protein 1 SLAIN motif family, SLAIN2 AI979301 0310 1.38052 57.75 1.38052 224854_s_at member 2 C-type lectin domain CLEC1B NM_016509 0902 1.57911 34.1712 1.57911 220496_at family 1, member B tetratricopeptide repeat TTC7A BE205790 0568 0.727973 −13.8295 −1.37368 224924_at domain 7A suppressor of Ty 16 SUPT16H AK024072 0341 1.40153 75.4675 1.40153 233827_s_at homolog (S. cerevisiae) SERPINE1 mRNA binding SERBP1 BC003049 0547 1.15454 187.371 1.15454 209669_s_at protein 1 RNA binding motif protein RBM14 AF315633 0153 0.669042 −19.7848 −1.49467 1555639_a_at 14 T-cell acute lymphocytic TAL1 NM_003189 0800 1.49187 67.9937 1.49187 206283_s_at leukemia 1 Ras association RAPH1 AA194149 0014 1.40811 13.9347 1.40811 225188_at (RalGDS/AF-6) and pleckstrin homology domains 1 disabled homolog 2, DAB2 N21202 0744 1.32324 23.7867 1.32324 201278_at mitogen-responsive phosphoprotein (Drosophila) v-ets erythroblastosis virus ETS1 NM_005238 0840 0.706997 −21.9256 −1.41443 214447_at E26 oncogene homolog 1 (avian) elastin microfibril EMILIN2 AL552384 0416 0.683088 −18.3855 −1.46394 242288_s_at interfacer 2 myosin IXB MYO9B NM_004145 0815 0.605039 −41.608 −1.65279 208452_x_at DnaJ (Hsp40) homolog, DNAJC13 BC043583 0562 1.40365 7.41601 1.40365 1560020_at subfamily C, member 13 acyl-Coenzyme A binding ACBD5 BC025309 0560 1.36451 22.651 1.36451 1568877_a_at domain containing 5 Ras association RAPH1 AA194149 0014 1.37974 8.71298 1.37974 225189_s_at (RalGDS/AF-6) and pleckstrin homology domains 1 C-type lectin domain CLEC4E BC000715 0538 0.686069 −379.336 −1.45758 222934_s_at family 4, member E Fc fragment of IgA, FCAR U43677 0983 0.627309 −37.9565 −1.59411 211307_s_at receptor for ATPase, Ca++ ATP2A3 AA877910 0076 0.702202 −30.8685 −1.42409 213042_s_at transporting, ubiquitous methionine MAT2A NM_005911 0848 0.808703 −23.1428 −1.23655 200769_s_at adenosyltransferase II, alpha general transcription factor GTF2A1 NM_015859 0891 1.61825 18.7636 1.61825 206521_s_at IIA, 1, 19/37 kDa DAZ associated protein 2 DAZAP2 AL534321 0411 0.83346 −337.118 −1.19982 212595_s_at chromosome 1 open C1orf38 AB035482 0091 0.788942 −371.48 −1.26752 210785_s_at reading frame 38 arrestin domain containing 1 ARRDC1 AK001822 0323 0.77686 −64.9423 −1.28723 226405_s_at RAD23 homolog B RAD23B AL527365 0409 0.742279 −173.664 −1.3472 201222_s_at (S. cerevisiae) chromosome 19 open C19orf6 AC004528 0097 0.649764 −51.5385 −1.53902 212574_x_at reading frame 6 procollagen-proline, 2- P4HB J02783 0716 0.859883 −245.237 −1.16295 200654_at oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide period homolog 1 PER1 AF022991 0108 0.772837 −21.3812 −1.29393 36829_at (Drosophila) galactosylceramidase GALC D25284 0705 0.843323 −10.2215 −1.18579 211810_s_at CDNA FLJ33748 fis, clone — H75391 0715 1.38204 16.1 1.38204 1559515_at BRCAN2000148 glucosamine (N-acetyl)-6- GNS NM_002076 0782 0.703894 −39.7323 −1.42067 203676_at sulfatase (Sanfilippo disease IIID) non-POU domain NONO L14599 0721 0.865461 −81.334 −1.15545 208698_s_at containing, octamer- binding zinc finger protein 117 ZNF117 NM_024498 0946 1.38949 39.4965 1.38949 207605_x_at activin A receptor, type IB ACVR1B AL117643 0384 0.842946 −32.3868 −1.18632 213198_at minichromosome MCM3AP AK022303 0333 0.720718 −11.7219 −1.38751 215581_s_at maintenance complex component 3 associated protein natural killer-tumor NKTR AA732581 0048 1.37587 41.4737 1.37587 231235_at recognition sequence sorbin and SH3 domain SORBS3 NM_005775 0844 0.609982 −17.4581 −1.63939 207788_s_at containing 3 phosphoinositide-3-kinase PIK3IP1 BE042976 0563 0.772434 −157.815 −1.29461 221757_at interacting protein 1 CDNA FLJ34061 fis, clone — BG430133 0695 1.46652 12.8086 1.46652 1565614_at FCBBF3000462 heterogeneous nuclear HNRNPC AV725195 0452 1.15559 262.504 1.15559 214737_x_at ribonucleoprotein C (C1/C2) calnexin CANX AI761759 0258 0.865197 −66.4295 −1.15581 208852_s_at inositol polyphosphate-5- INPP5D U53470 0985 0.782311 −68.532 −1.27826 203331_s_at phosphatase, 145 kDa hepatocellular carcinoma- HCRP1 AK025343 0356 0.78604 −15.3697 −1.2722 216174_at related HCRP1 solute carrier family 12 SLC12A9 BC000154 0535 0.668443 −33.1179 −1.49601 223994_s_at (potassium/chloride transporters), member 9 suppression of ST14 U20428 0979 0.688211 −10.2143 −1.45304 216905_s_at tumorigenicity 14 (colon carcinoma) plasminogen activator, PLAUR U08839 0975 0.739167 −184.938 −1.35287 210845_s_at urokinase receptor TAF8 RNA polymerase II, TAF8 BU618741 0703 0.815823 −13.4618 −1.22576 1556178_x_at TATA box binding protein (TBP)-associated factor, 43 kDa chemokine (C—X—C motif) CXCR4 L01639 0719 0.831693 −306.096 −1.20237 209201_x_at receptor 4 N-acetylglucosamine-1- GNPTG AF302786 0151 0.864971 −27.9294 −1.15611 224887_at phosphate transferase, gamma subunit protein associated with PATL1 AA359612 0018 0.827113 −15.0724 −1.20902 235235_s_at topoisomerase II homolog 1 (yeast) galactosidase, beta 1 GLB1 NM_000404 0758 0.862277 −81.7493 −1.15972 201576_s_at PDZ and LIM domain 2 PDLIM2 NM_021630 0934 0.854149 −92.4219 −1.17076 219165_at (mystique) (clone 1NIB-4) normalized — BQ002274 0702 0.660567 −10.368 −1.51385 1556314_a_at cDNA library sequence transmembrane protein 43 TMEM43 W74580 1000 0.844907 −80.8659 −1.18356 217795_s_at exosome component 1 EXOSC1 BC012538 0559 1.32212 9.35476 1.32212 1559044_at transducin-like enhancer TLE4 AL358975 0400 0.843292 −38.0674 −1.18583 216997_x_at of split 4 (E(sp1) homolog, Drosophila) plectin 1, intermediate PLEC1 Z54367 1015 0.708741 −39.4505 −1.41095 216971_s_at filament binding protein 500 kDa FIP1 like 1 (S. cerevisiae) FIP1L1 NM_030917 0957 1.12041 21.6845 1.12041 221007_s_at blocked early in transport BET1L NM_016526 0903 0.428008 −16.7549 −2.3364 220470_at 1 homolog (S. cerevisiae)- like SMEK homolog 1, SMEK1 NM_017936 0917 1.29938 20.9668 1.29938 220369_at suppressor of mek1 (Dictyostelium) nuclear casein kinase and NUCKS1 AW515443 0516 1.25494 203.425 1.25494 229353_s_at cyclin-dependent kinase substrate 1 myosin IXB MYO9B AF143684 0137 0.706462 −125.22 −1.4155 217297_s_at zinc finger RNA binding ZFR AI459274 0207 1.35041 23.441 1.35041 33148_at protein chromosome 8 open C8orf42 AI632224 0222 1.55823 7.12392 1.55823 226778_at reading frame 42 retinol saturase (all-trans- RETSAT AK098125 0364 0.74181 −13.5564 −1.34805 1566472_s_at retinol 13,14-reductase) protein kinase, AMP- PRKAB2 NM_005399 0841 1.31212 10.5339 1.31212 214474_at activated, beta 2 non- catalytic subunit U2 small nuclear RNA U2AF2 NM_007279 0875 0.730157 −41.0539 −1.36957 218382_s_at auxiliary factor 2 WD repeat domain 1 WDR1 AF274954 0150 0.711232 −167.701 −1.40601 210935_s_at PTK2 protein tyrosine PTK2 AL037339 0368 1.23432 13.9745 1.23432 208820_at kinase 2 solute carrier family 16, SLC16A3 AL513917 0404 0.653057 −197.651 −1.53126 202855_s_at member 3 (monocarboxylic acid transporter 4) tripartite motif-containing 8 TRIM8 NM_030912 0956 1.187 123.174 1.187 221012_s_at Full-length cDNA clone — AW953794 0525 0.713306 −10.9193 −1.40192 230968_at CS0DF032YA11 of Fetal brain of Homo sapiens (human) speckle-type POZ protein SPOP NM_003563 0805 1.10986 90.8075 1.10986 204640_s_at BCL2-associated X BAX U19599 0977 0.756064 −36.9248 −1.32264 211833_s_at protein high mobility group AT- HMGA1 AF176039 0141 0.563365 −17.5088 −1.77505 210457_x_at hook 1 Transcribed locus — BE348304 0572 1.31402 13.2065 1.31402 237554_at transmembrane and TMCO3 NM_017905 0914 0.795943 −17.5981 −1.25637 220240_s_at coiled-coil domains 3 C-type lectin domain CLEC4E NM_014358 0885 0.75634 −49.143 −1.32216 219859_at family 4, member E chromosome 7 open C7orf27 AK024482 0345 0.762591 −31.4652 −1.31132 225437_s_at reading frame 27 suppressor of zeste 12 SUZ12 /// AI924660 0297 1.16535 41.8695 1.16535 213971_s_at homolog (Drosophila) /// SUZ12P suppressor of zeste 12 homolog pseudogene unc-93 homolog B1 (C. elegans) UNC93B1 NM_030930 0959 0.676621 −42.7644 −1.47793 220998_s_at Transcribed locus, — AI738675 0248 0.781337 −110.327 −1.27986 240064_at strongly similar to XP_529518.1 PREDICTED: hypothetical protein XP_529518 [Pan troglodytes] differentially expressed in DEF6 NM_022047 0937 0.84778 −51.5421 −1.17955 221293_s_at FDCP 6 homolog (mouse) KIAA0146 KIAA0146 AI363213 0191 0.719196 −31.4259 −1.39044 228325_at BCL6 co-repressor BCOR AF317392 0154 1.4648 35.2478 1.4648 223916_s_at KIAA0319-like KIAA0319L W58365 0999 0.753732 −120.246 −1.32673 222468_at — — AK000677 0317 1.3013 14.5053 1.3013 233876_at ADP-dependent ADPGK BC006112 0557 0.844025 −25.0846 −1.1848 224455_s_at glucokinase TSC22 domain family, TSC22D3 AL110191 0382 0.786558 −926.021 −1.27136 208763_s_at member 3 nemo-like kinase NLK NM_016231 0897 1.17576 12.9069 1.17576 218318_s_at amyloid beta (A4) APLP2 AW001847 0461 0.766817 −206.16 −1.30409 214875_x_at precursor-like protein 2 phospholipase D family, PLD3 NM_012268 0878 0.696935 −82.8652 −1.43485 201050_at member 3 Transcribed locus — BF114745 0621 1.12277 11.3237 1.12277 235459_at ER lipid raft associated 1 ERLIN1 AL568449 0419 0.852824 −58.6846 −1.17257 202441_at Transcribed locus — H24473 0713 1.34485 6.82582 1.34485 229951_x_at procollagen-proline, 2- P4HB NM_000918 0762 0.881299 −107.084 −1.13469 200656_s_at oxoglutarate 4- dioxygenase (proline 4- hydroxylase), beta polypeptide calreticulin CALR BE251303 0570 0.767097 −108.355 −1.30362 212953_x_at PTK2B protein tyrosine PTK2B NM_004103 0812 0.665846 −51.1597 −1.50185 203111_s_at kinase 2 beta KIAA0892 KIAA0892 AC003030 0096 0.554142 −12.142 −1.80459 216926_s_at angiotensin II receptor- AGTRAP AF165187 0139 0.774605 −168.031 −1.29098 1555736_a_at associated protein Transcribed locus — AW244016 0490 0.671508 −53.1796 −1.48918 227762_at Full length insert cDNA — AF086041 0124 1.45973 23.1829 1.45973 1556812_a_at clone YX53E08 suppression of ST14 NM_021978 0936 0.644679 −20.0323 −1.55116 202005_at tumorigenicity 14 (colon carcinoma) serologically defined colon SDCCAG1 BC006001 0556 1.18167 63.5301 1.18167 1569594_a_at cancer antigen 1 Cbp/p300-interacting CITED2 NM_006079 0852 0.840662 −48.6818 −1.18954 207980_s_at transactivator, with Glu/Asp-rich carboxy- terminal domain, 2 ankyrin repeat and FYVE ANKFY1 NM_016376 0901 0.800364 −21.4969 −1.24943 219868_s_at domain containing 1 interleukin 13 receptor, IL13RA1 NM_001560 0773 0.812748 −147.49 −1.23039 201887_at alpha 1 EH domain binding protein EHBP1L1 AA149545 0012 0.779588 −73.7409 −1.28273 91703_at 1-like 1 Rho GTPase activating ARHGAP4 NM_001666 0777 0.768348 −61.7389 −1.30149 204425_at protein 4 Transcribed locus — AW298731 0504 0.557986 −21.7775 −1.79216 239249_at Ras and Rab interactor 3 RIN3 AW027923 0470 0.727238 −60.7916 −1.37507 219456_s_at CDNA clone — N57510 0749 1.15693 17.2711 1.15693 234998_at IMAGE: 5313062 Homo sapiens, clone — AV735241 0455 1.18015 26.1526 1.18015 225055_at IMAGE: 3345917, mRNA pro-platelet basic protein PPBP R64130 0963 1.67072 1663.59 1.67072 214146_s_at (chemokine (C—X—C motif) ligand 7) cell division cycle 2-like 1 CDC2L1 /// NM_001787 0779 0.850597 −29.5012 −1.17564 207428_x_at (PITSLRE proteins) /// cell CDC2L2 division cycle 2-like 2 (PITSLRE proteins) cysteine conjugate-beta CCBL2 BC000819 0540 1.1738 47.6813 1.1738 209472_at lyase 2 sema domain, SEMA4A NM_022367 0939 0.732766 −132.251 −1.36469 219259_at immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A Rho GDP dissociation ARHGDIA D13989 0704 0.45839 −116.893 −2.18155 201167_x_at inhibitor (GDI) alpha Wolf-Hirschhorn syndrome WHSC1L1 NM_017778 0912 1.19614 11.2303 1.19614 218173_s_at candidate 1-like 1 tissue factor pathway TFPI AF021834 0107 1.72078 9.20714 1.72078 210664_s_at inhibitor (lipoprotein- associated coagulation inhibitor) zinc finger protein 271 ZNF271 AF159567 0138 1.1964 29.3872 1.1964 211009_s_at Wiskott-Aldrich syndrome WAS NM_000377 0757 0.447977 −226.867 −2.23226 205400_at (eczema- thrombocytopenia) EH domain binding protein 1 EHBP1 BF116032 0624 1.40606 28.0113 1.40606 212650_at solute carrier family 6 SLC6A6 U16120 0976 0.713183 −24.4459 −1.40216 205921_s_at (neurotransmitter transporter, taurine), member 6 ADAM metallopeptidase ADAM8 AI814527 0277 0.541261 −101.711 −1.84754 205179_s_at domain 8 zinc finger protein 36, C3H ZFP36L2 AI356398 0189 0.570918 −423.25 −1.75157 201367_s_at type-like 2 RAB27B, member RAS RAB27B BF438386 0637 1.3631 49.8935 1.3631 228708_at oncogene family versican VCAN D32039 0706 0.776785 −306.325 −1.28736 211571_s_at Interleukin 8 IL8 AJ239383 0313 0.627373 −44.5734 −1.59395 217281_x_at leukocyte immunoglobulin- LILRA2 U82277 0993 0.700637 −149.21 −1.42727 211102_s_at like receptor, subfamily A (with TM domain), member 2 immunoglobulin heavy IGH@ /// S55735 0965 0.559124 −2082.58 −1.78851 217022_s_at locus /// immunoglobulin IGHA1 /// heavy constant alpha 1 /// IGHA2 /// immunoglobulin heavy LOC100126583 constant alpha 2 (A2m marker) /// hypothetical LOC100126583 regulator of G-protein RGS14 AF037194 0109 0.684164 −37.2156 −1.46164 211021_s_at signaling 14 F-box protein 9 FBXO9 AK095315 0363 1.35494 283.431 1.35494 1566509_s_at septin 9 9-Sep NM_006640 0865 0.530246 −77.4496 −1.88592 207425_s_at myeloid cell leukemia MCL1 NM_021960 0935 0.820331 −746.654 −1.21902 200798_x_at sequence 1 (BCL2- related) poly(A) polymerase alpha PAPOLA BF797555 0662 1.21671 261.98 1.21671 212718_at Transcribed locus — AI492388 0212 0.619996 −132.97 −1.61291 228854_at Rho GDP dissociation ARHGDIA AI571798 0218 0.435657 −122.614 −2.29538 213606_s_at inhibitor (GDI) alpha guanine nucleotide GNAZ NM_002073 0781 1.6445 54.2522 1.6445 204993_at binding protein (G protein), alpha z polypeptide ATPase, Ca++ ATP2A3 AF068220 0120 0.668956 −47.3043 −1.49487 207521_s_at transporting, ubiquitous prostaglandin- PTGS1 BE613133 0580 1.56705 100.206 1.56705 238669_at endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) ankyrin repeat and BTB ABTB1 AW511257 0514 0.643482 −21.8363 −1.55405 228848_at (POZ) domain containing 1 folate receptor 1 (adult) FOLR1 AF000381 0102 1.40192 561.562 1.40192 211074_at Fc fragment of IgA, FCAR NM_002000 0780 0.718362 −69.5336 −1.39206 207674_at receptor for G-protein signaling GPSM3 BG111168 0671 0.600035 −318.6 −1.66657 214847_s_at modulator 3 (AGS3-like, C. elegans) Spermatid perinuclear STRBP AK024960 0353 1.48647 14.4948 1.48647 233251_at RNA binding protein enoyl Coenzyme A ECHDC3 NM_024693 0948 0.620987 −37.4804 −1.61034 219298_at hydratase domain containing 3 heterogeneous nuclear HNRNPC NM_004500 0824 1.12397 173.739 1.12397 200014_s_at ribonucleoprotein C (C1/C2) colony stimulating factor 3 CSF3R NM_000760 0761 0.75872 −966.201 −1.31801 203591_s_at receptor (granulocyte) myosin, light chain 6, MYL6 BE734356 0594 1.21794 1025.74 1.21794 212082_s_at alkali, smooth muscle and non-muscle strawberry notch homolog SBNO2 AC005390 0100 0.649244 −68.1785 −1.54025 215760_s_at 2 (Drosophila) DEAD (Asp-Glu-Ala-Asp) DDX17 AA521056 0025 1.25593 661.69 1.25593 230180_at box polypeptide 17 amyotrophic lateral ALS2CR12 AI057333 0163 1.98348 45.6236 1.98348 239458_at sclerosis 2 (juvenile) chromosome region, candidate 12 egl nine homolog 2 (C. elegans) EGLN2 AW057545 0472 0.576276 −34.3406 −1.73528 223083_s_at WD and tetratricopeptide WDTC1 AK001734 0321 0.665423 −71.9458 −1.5028 216036_x_at repeats 1 CD74 molecule, major CD74 M28590 0733 0.600568 −261.5 −1.66509 1567628_at histocompatibility complex, class II invariant chain glycoprotein VI (platelet) GP6 AB043821 0092 1.54831 33.695 1.54831 220336_s_at dual specificity DUSP1 AA530892 0027 0.512623 −102.105 −1.95075 201044_x_at phosphatase 1 transcription factor binding TFE3 AY034078 0534 0.603333 −38.6627 −1.65746 1565347_s_at to IGHM enhancer 3 gelsolin (amyloidosis, GSN BE675337 0587 0.650402 −41.5488 −1.53751 214040_s_at Finnish type) guanine nucleotide GNG11 NM_004126 0814 1.61366 208.508 1.61366 204115_at binding protein (G protein), gamma 11 CD6 molecule CD6 NM_006725 0867 0.611045 −58.7246 −1.63654 208602_x_at nerve growth factor NGFRAP1 NM_014380 0886 1.38676 192.886 1.38676 217963_s_at receptor (TNFRSF16) associated protein 1 selectin P ligand SELPLG AI741056 0250 0.832688 −546.812 −1.20093 209879_at CD44 molecule (Indian CD44 AF098641 0127 0.856847 −61.9943 −1.16707 210916_s_at blood group) ORAI calcium release- ORAI2 BF939788 0663 0.633836 −34.2127 −1.57769 218811_at activated calcium modulator 2 prosaposin (variant PSAP M32221 0734 0.846847 −996.693 −1.18085 200866_s_at Gaucher disease and variant metachromatic leukodystrophy) cortactin CTTN NM_005231 0839 1.50296 60.9429 1.50296 201059_at CD6 molecule CD6 U66145 0988 0.651121 −57.9464 −1.53581 211893_x_at potassium voltage-gated KCNAB2 AF044253 0112 0.575621 −23.6953 −1.73725 211791_s_at channel, shaker-related subfamily, beta member 2 tyrosine 3- YWHAZ NM_003406 0803 1.16412 488.217 1.16412 200639_s_at monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide prefoldin subunit 5 PFDN5 NM_002624 0793 1.42957 326.46 1.42957 207132_x_at zinc finger E-box binding ZEB2 AV739670 0456 1.5295 31.1939 1.5295 233031_at homeobox 2 lymphocyte-specific LSP1 NM_002339 0784 0.76397 −707.2 −1.30895 203523_at protein 1 GM2 ganglioside activator GM2A AL513583 0403 0.724236 −112.384 −1.38076 212737_at B-cell CLL/lymphoma 3 BCL3 AI829875 0287 0.59887 −49.0698 −1.66981 204907_s_at signal-regulatory protein SIRPA AC004832 0099 0.575913 −48.7608 −1.73637 217024_x_at alpha chromosome 21 open C21orf7 NM_020152 0932 1.55157 99.5819 1.55157 221211_s_at reading frame 7 arachidonate 12- ALOX12 NM_000697 0760 1.54212 50.2344 1.54212 207206_s_at lipoxygenase immunoglobulin heavy IGHD AJ275469 0314 0.637582 −65.6509 −1.56843 214973_x_at constant delta signal-regulatory protein SIRPA NM_004648 0827 0.815813 −62.6483 −1.22577 202896_s_at alpha talin 1 TLN1 NM_006289 0857 0.703842 −284.992 −1.42077 203254_s_at versican VCAN R94644 0964 0.821433 −285.21 −1.21738 215646_s_at leukocyte immunoglobulin- LILRA4 AF041261 0110 0.699309 −21.5601 −1.42998 210313_at like receptor, subfamily A (with TM domain), member 4 dual specificity DUSP1 NM_004417 0823 0.742647 −870.146 −1.34654 201041_s_at phosphatase 1 leukocyte immunoglobulin- LILRA2 U82278 0994 0.798914 −260.133 −1.2517 211100_x_at like receptor, subfamily A (with TM domain), member 2 leukocyte immunoglobulin- LILRA2 U82276 0992 0.79042 −238.501 −1.26515 211101_x_at like receptor, subfamily A (with TM domain), member 2 colony stimulating factor 3 CSF3R NM_172313 0960 0.808882 −920.479 −1.23627 1553297_a_at receptor (granulocyte) immunoglobulin lambda IGL@ D87021 0711 0.568492 −34.0245 −1.75904 216560_x_at locus opioid growth factor OGFR AF172449 0140 0.675188 −26.4472 −1.48107 211513_s_at receptor BCL2-associated BAG1 NM_004323 0820 1.33534 836.698 1.33534 202387_at athanogene tetraspanin 5 TSPAN5 AF065389 0119 1.41793 336.467 1.41793 209890_at platelet factor 4 PF4 NM_002619 0791 1.45302 929.754 1.45302 206390_x_at (chemokine (C—X—C motif) ligand 4) Fc fragment of IgA, FCAR U56237 0986 0.692035 −10.089 −1.44501 211306_s_at receptor for transketolase (Wernicke- TKT BF696840 0656 0.825852 −541.902 −1.21087 208699_x_at Korsakoff syndrome) heterogeneous nuclear HNRNPC AA664258 0039 1.15573 239.689 1.15573 212626_x_at ribonucleoprotein C (C1/C2) tumor necrosis factor TNFRSF10C NM_003841 0808 0.710572 −502.391 −1.40732 206222_at receptor superfamily, member 10c, decoy without an intracellular domain clusterin CLU M25915 0732 1.56445 331.206 1.56445 208792_s_at Interleukin 8 IL8 L34164 0723 0.606145 −44.8057 −1.64977 211650_x_at chromosome Y open CYorf15A AW468885 0510 1.86697 28.7205 1.86697 236694_at reading frame 15A insulin-like growth factor 1 IGF1R BF347362 0633 0.713503 −8.93807 −1.40154 243358_at receptor Immunoglobulin heavy IGHG1 M24668 0731 0.640653 −24.0473 −1.56091 211633_x_at constant gamma 1 (G1m marker) adducin 3 (gamma) ADD3 AI763123 0262 1.10373 199.209 1.10373 201752_s_at GM2 ganglioside activator GM2A M76477 0737 0.549282 −17.8258 −1.82056 209727_at small EDRK-rich factor 2 SERF2 BE568651 0579 1.18189 762.518 1.18189 224625_x_at neurofilament, light NEFL AL537457 0413 1.38097 8.81215 1.38097 221805_at polypeptide 68 kDa hypothetical protein LOC284701 AL137733 0398 0.575711 −47.8667 −1.73698 234664_at LOC284701 interferon regulatory factor 7 IRF7 NM_004030 0810 0.656921 −213.859 −1.52225 208436_s_at CTD (carboxy-terminal CTDSPL NM_005808 0846 1.50567 31.4589 1.50567 201906_s_at domain, RNA polymerase II, polypeptide A) small phosphatase-like immunoglobulin heavy IGHA1 /// U92706 0997 0.654147 −45.8457 −1.52871 216557_x_at constant alpha 1 /// IGHG1 /// immunoglobulin heavy IGHG3 /// constant gamma 1 (G1m IGHM /// marker) /// immunoglobulin IGHV4-31 heavy constant gamma 3 (G3m marker) /// immunoglobulin heavy constant mu /// immunoglobulin heavy variable 4-31 calreticulin CALR NM_004343 0821 0.666427 −39.7641 −1.50054 200935_at profilin 1 PFN1 NM_005022 0834 0.909933 −688.243 −1.09898 200634_at GM2 ganglioside activator GM2A M76477 0737 0.760155 −51.1178 −1.31552 35820_at Immunoglobulin heavy IGHA1 AW519168 0517 0.696459 −66.6484 −1.43583 215118_s_at constant alpha 1 BCL2-associated BAG1 AF116273 0132 1.29366 745.959 1.29366 211475_s_at athanogene integrin, beta 2 ITGB2 NM_000211 0756 0.904719 −606.678 −1.10532 202803_s_at (complement component 3 receptor 3 and 4 subunit) integral membrane protein ITM2B AF092128 0126 0.920192 −904.73 −1.08673 217732_s_at 2B myeloid cell leukemia MCL1 AI275690 0180 0.920558 −557.764 −1.0863 200797_s_at sequence 1 (BCL2- related) GNAS complex locus GNAS AA650558 0038 1.28011 328.574 1.28011 217673_x_at tubulin, beta 1 TUBB1 N63244 0750 1.30121 525.72 1.30121 230690_at ribosomal protein L23 RPL23 NM_000978 0767 1.38751 582.376 1.38751 200888_s_at peroxiredoxin 6 PRDX6 BE869583 0604 1.29349 781.185 1.29349 200844_s_at neurofilament, light NEFL BF055311 0613 1.33283 20.5017 1.33283 221916_at polypeptide 68 kDa immunoglobulin kappa IGK@ /// IGKC AW575927 0518 0.828408 −1002.05 −1.20713 224795_x_at constant /// /// IGKV1-5 /// immunoglobulin kappa IGKV2-24 variable 1-5 /// immunoglobulin kappa variable 2-24 /// immunoglobulin kappa locus cystatin C (amyloid CST3 NM_000099 0755 0.839452 −682.022 −1.19125 201360_at angiopathy and cerebral hemorrhage) ribosomal protein L7 RPL7 NM_000971 0766 1.25494 1233.19 1.25494 200717_x_at interferon induced IFITM1 AA749101 0057 0.874523 −1026.24 −1.14348 214022_s_at transmembrane protein 1 (9-27) ribosomal protein L36a /// LOC729362 /// NM_021029 0933 1.40994 1319.28 1.40994 201406_at similar to large subunit RPL36A ribosomal protein L36a SUB1 homolog (S. cerevisiae) SUB1 BE784583 0598 1.28695 310.449 1.28695 224586_x_at guanylate kinase 1 GUK1 BC006249 0558 1.2612 828.435 1.2612 200075_s_at Pre-B-cell colony PBEF1 AA873350 0074 0.851427 −574.61 −1.1745 243296_at enhancing factor 1 prostaglandin- PTGS1 NM_000962 0764 1.30351 24.1075 1.30351 205127_at endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) F-box protein 7 FBXO7 NM_012179 0877 1.21038 1054.96 1.21038 201178_at hemoglobin, alpha 1 /// HBA1 /// HBA2 AF105974 0128 1.31542 1468.63 1.31542 209458_x_at hemoglobin, alpha 2 hemoglobin, alpha 1 HBA1 BC005931 0555 1.32226 1497.18 1.32226 211745_x_at immunoglobulin lambda IGL@ /// IGLJ3 X57812 1008 0.781053 −974.535 −1.28032 214677_x_at locus /// immunoglobulin /// IGLV2-14 /// lambda variable 4-3 /// IGLV3-25 /// immunoglobulin lambda IGLV4-3 variable 3-25 /// immunoglobulin lambda variable 2-14 /// immunoglobulin lambda joining 3 major histocompatibility HLA-G M90686 0740 0.800128 −1437.74 −1.2498 211530_x_at complex, class I, G SUB1 homolog (S. cerevisiae) SUB1 BG231551 0678 1.25347 405.331 1.25347 212857_x_at chemokine (C—X3—C motif) CX3CR1 U20350 0978 1.14315 339.788 1.14315 205898_at receptor 1 metastasis associated MALAT1 AF132202 0134 0.892637 −753.262 −1.12028 223940_x_at lung adenocarcinoma transcript 1 (non-protein coding) metastasis associated MALAT1 BG534952 0699 1.12359 745.361 1.12359 224567_x_at lung adenocarcinoma transcript 1 (non-protein coding) tubulin, beta 2A TUBB2A NM_001069 0768 1.79577 548.832 1.79577 204141_at solute carrier family 25, SLC25A37 BG251467 0679 1.09794 685.472 1.09794 222529_at member 37 solute carrier family 25, SLC25A37 BG251467 0679 1.16922 684.917 1.16922 222528_s_at member 37 GNAS complex locus GNAS NM_016592 0905 1.06718 381.104 1.06718 200981_x_at metastasis associated MALAT1 BE708432 0592 1.04778 706.89 1.04778 1558678_s_at lung adenocarcinoma transcript 1 (non-protein coding)

TABLE 2A t-Test Fold Change Log10 Known Genbank SEQ p-Value Signed Mean Fragment Genes: Gene Accession ID Sequence Clusters: (MS vs Magnitude (MS FC (Control Name Symbol No. NO. Cluster Title Control) vs. Control) Magnitude Samples) 214847_s_at GPSM3 BG111168 0671 “G-protein signalling 1.29E−11 1.82 1.82 2.2 modulator 3 (AGS3-like, C. elegans)” 227510_x_at AL037917 0369 Transcribed locus 1.41E−10 6.2 6.2 2.29 223578_x_at MALAT1 AF113016 0131 Metastasis associated 1.55E−10 3.4 3.4 1.83 lung adenocarcinoma transcript 1 (non-coding RNA) 232431_at AI934556 0302 “Glucocorticoid receptor 4.46E−10 −2.75 2.75 2.52 alpha mRNA, variant 3′ UTR” 219878_s_at KLF13 NM_015995 0892 Kruppel-like factor 13 8.23E−10 13.42 13.42 0.4 214352_s_at KRAS BF673699 0652 V-Ki-ras2 Kirsten rat 1.04E−09 2.25 2.25 2.06 sarcoma viral oncogene homolog 228582_x_at MALAT1 AI475544 0211 Metastasis associated 1.06E−09 9.68 9.68 2.39 lung adenocarcinoma transcript 1 (non-coding RNA) 243981_at AI763206 0263 Transcribed locus 1.42E−09 −2.43 2.43 2.5 201753_s_at ADD3 NM_019903 0931 Adducin 3 (gamma) 1.95E−09 −1.85 1.85 3.16 211074_at FOLR1 AF000381 0102 Folate receptor 1 (adult) 3.38E−09 2.39 2.39 2.16 225956_at LOC153222 AL565238 0417 Adult retina protein 3.62E−09 −1.48 1.48 2.87 223161_at KIAA1147 AA029331 0003 KIAA1147 4.65E−09 2.34 2.34 2.27 218389_s_at APH1A NM_016022 0894 Anterior pharynx defective 4.69E−09 1.51 1.51 2.26 1 homolog A (C. elegans) 236924_at GLMN AA814383 0065 “Glomulin, FKBP 7.55E−09 −2.5 2.5 2.05 associated protein” 226148_at ZBTB44 AU144305 0422 Zinc finger and BTB 1.05E−08 −1.78 1.78 2.96 domain containing 44 219696_at FLJ20054 NM_019049 0927 Hypothetical protein 1.10E−08 −1.47 1.47 2.18 FLJ20054 223940_x_at AF132202 0134 1.32E−08 2.92 2.92 2.45 225889_at AEBP2 BF475280 0639 AE binding protein 2 1.37E−08 −1.88 1.88 2.69 214697_s_at ROD1 AW190873 0485 ROD1 regulator of 1.71E−08 2.27 2.27 1.9 differentiation 1 (S. pombe) 208610_s_at SRRM2 AI655799 0233 Serine/arginine repetitive 2.18E−08 3.16 3.16 1.72 matrix 2 241751_at OFD1 AW292752 0498 Oral-facial-digital 2.26E−08 −2.4 2.4 2.17 syndrome 1 204049_s_at PHACTR2 NM_014721 0889 Phosphatase and actin 3.26E−08 −1.7 1.7 2.33 regulator 2 225377_at C9orf86 BE783949 0597 Chromosome 9 open 3.78E−08 1.9 1.9 2.27 reading frame 86 225139_at RBM35B AW070424 0473 RNA binding motif protein 3.81E−08 −1.6 1.6 3 35B 216177_at LOC391132 AW582267 0519 Similar to 60S ribosomal 3.88E−08 −1.88 1.88 2.19 protein L29 (P23) 242232_at AI652864 0232 4.50E−08 2.15 2.15 1.7 200734_s_at ARF3 BG341906 0689 ADP-ribosylation factor 3 4.57E−08 1.78 1.78 2.25 211716_x_at ARHGDIA BC005851 0554 Rho GDP dissociation 4.64E−08 1.66 1.66 2.62 inhibitor (GDI) alpha 215460_x_at BRD1 AL080149 0380 Bromodomain containing 1 4.65E−08 −1.39 1.39 2.25 222576_s_at EIF2C1 AW071829 0475 “Eukaryotic translation 4.71E−08 1.88 1.88 2.14 initiation factor 2C, 1” 230141_at ARID4A AI640594 0226 AT rich interactive domain 5.62E−08 −1.88 1.88 2.19 4A (RBP1-like) 227740_at UHMK1 AW173222 0481 U2AF homology motif 5.74E−08 2.45 2.45 2.37 (UHM) kinase 1 204805_s_at H1FX NM_006026 0851 “H1 histone family, 6.56E−08 2.3 2.3 2.26 member X” 208624_s_at EIF4G1 BE966878 0610 “Eukaryotic translation 6.81E−08 1.41 1.41 1.88 initiation factor 4 gamma, 1” 243612_at NSD1 AL526448 0408 Nuclear receptor binding 7.09E−08 −2.61 2.61 2.19 SET domain protein 1 201167_x_at ARHGDIA D13989 0704 Rho GDP dissociation 7.24E−08 2.48 2.48 1.72 inhibitor (GDI) alpha 241786_at AI380514 0198 Transcribed locus 7.33E−08 −2.3 2.3 2.61 238430_x_at SLFN5 AI923675 0295 Schlafen family member 5 7.41E−08 2.67 2.67 2.57 202102_s_at BRD4 BF718610 0657 Bromodomain containing 4 7.45E−08 1.54 1.54 2.32 201737_s_at MARCH6 NM_005885 0847 Membrane-associated 8.45E−08 −1.77 1.77 2.53 ring finger (C3HC4) 6 229926_at AI633738 0225 Transcribed locus 8.49E−08 −1.61 1.61 2.04 230961_at BE856980 0603 9.10E−08 −2.05 2.05 2.07 201996_s_at SPEN AL524033 0406 “Spen homolog, 9.12E−08 2.59 2.59 1.55 transcriptional regulator (Drosophila)” 231858_x_at DKFZp761E198 BC004895 0552 DKFZp761E198 protein 9.89E−08 1.83 1.83 2.02 200608_s_at RAD21 NM_006265 0855 RAD21 homolog (S. pombe) 9.99E−08 −1.44 1.44 2.61 201168_x_at ARHGDIA NM_004309 0818 Rho GDP dissociation 1.00E−07 1.81 1.81 2.37 inhibitor (GDI) alpha 224631_at ZFP91 AA758013 0058 Zinc finger protein 91 1.00E−07 1.92 1.92 2.02 homolog (mouse) 225563_at PAN3 AI970788 0309 PAN3 polyA specific 1.05E−07 −1.62 1.62 3.03 ribonuclease subunit homolog (S. cerevisiae) 222133_s_at PHF20L1 AK022280 0332 PHD finger protein 20-like 1 1.09E−07 −1.61 1.61 2.12 237768_x_at AA825925 0066 1.10E−07 −2.29 2.29 2.57 208677_s_at BSG AL550657 0415 Basigin (Ok blood group) 1.16E−07 2.21 2.21 1.92 224572_s_at IRF2BP2 BG485163 0697 Interferon regulatory factor 1.36E−07 2.35 2.35 2.63 2 binding protein 2 221899_at PFAAP5 AI809961 0274 Phosphonoformate 1.37E−07 −1.92 1.92 2.5 immuno-associated protein 5 224969_at ATXN7L3 AL390158 0401 Ataxin 7-like 3 1.45E−07 1.65 1.65 2.32 229389_at ATG16L2 AA741058 0050 ATG16 autophagy related 1.46E−07 3 3 2.32 16-like 2 (S. cerevisiae) 242134_at AI733194 0247 Transcribed locus 1.50E−07 2.2 2.2 1.72 224676_at TMED4 AI472339 0208 Transmembrane emp24 1.52E−07 2.09 2.09 2.45 protein transport domain containing 4 224568_x_at MALAT1 AW005982 0462 Metastasis associated 1.60E−07 3.14 3.14 2.28 lung adenocarcinoma transcript 1 (non-coding RNA) 218659_at ASXL2 NM_018263 0923 Additional sex combs like 1.65E−07 −1.46 1.46 2.88 2 (Drosophila) 203497_at PPARBP NM_004774 0829 PPAR binding protein 1.68E−07 −1.57 1.57 2.4 204285_s_at PMAIP1 AI857639 0288 Phorbol-12-myristate-13- 1.74E−07 2.56 2.56 1.82 acetate-induced protein 1 213015_at BF448315 0638 “ARTC1 mRNA, complete 1.93E−07 2.51 2.51 1.95 sequence” 224567_x_at MALAT1 BG534952 0699 Metastasis associated 1.95E−07 2.79 2.79 2.47 lung adenocarcinoma transcript 1 (non-coding RNA) 222790_s_at RSBN1 AK022166 0330 Round spermatid basic 2.00E−07 −2.2 2.2 2.87 protein 1 207057_at SLC16A7 NM_004731 0828 “Solute carrier family 16, 2.09E−07 4.01 4.01 1.41 member 7 (monocarboxylic acid transporter 2)” 212852_s_at TROVE2 AL538601 0414 “TROVE domain family, 2.09E−07 −1.44 1.44 2.61 member 2” 238761_at BE645241 0581 2.13E−07 −2.49 2.49 2.86 214198_s_at DGCR2 AU150824 0430 DiGeorge syndrome 2.16E−07 −1.66 1.66 2.25 critical region gene 2 202809_s_at INTS3 NM_023015 0943 Integrator complex subunit 3 2.18E−07 −1.26 1.26 2.19 236072_at N64578 0751 Transcribed locus 2.23E−07 −2.3 2.3 1.91 225827_at EIF2C2 AI832074 0288 “Eukaryotic translation 2.28E−07 2.51 2.51 2.14 initiation factor 2C, 2” 241775_at AW298119 0502 “CDNA FLJ26437 fis, 2.37E−07 −2.2 2.2 2.5 clone KDN02067” 215706_x_at ZYX BC002323 0543 Zyxin 2.42E−07 1.68 1.68 2.6 201730_s_at TPR BF110993 0619 Translocated promoter 2.44E−07 1.77 1.77 2.29 region (to activated MET oncogene) 226447_at ASH1L BG290742 0687 “Ash1 (absent, small, or 2.55E−07 −1.52 1.52 2.6 homeotic)-like (Drosophila)” 200623_s_at CALM3 MM_005184 0836 “Calmodulin 3 2.82E−07 1.87 1.87 2.33 (phosphorylase kinase, delta)” 215990_s_at BCL6 S67779 0966 B-cell CLL/lymphoma 6 2.92E−07 1.96 1.96 1.8 (zinc finger protein 51) 212007_at UBXD2 AI927512 0301 UBX domain containing 2 3.02E−07 1.5 1.5 2.05 225885_at EEA1 AI336848 0183 Early endosome antigen 1 3.04E−07 −1.63 1.63 2.5 212629_s_at PKN2 AI633689 0224 Protein kinase N2 3.06E−07 1.66 1.66 1.83 216971_s_at PLEC1 Z54367 1015 “Plectin 1, intermediate 3.10E−07 3.34 3.34 1.55 filament binding protein 500 kDa” 225289_at STAT3 AI139252 0174 Signal transducer and 3.15E−07 1.58 1.58 2.62 activator of transcription 3 (acute-phase response factor) 217713_x_at AA126763 0008 3.42E−07 −1.62 1.62 2.22 225361_x_at FAM122B AI348001 0187 Family with sequence 3.69E−07 −1.44 1.44 2.8 similarity 122B 242920_at AW590838 0520 3.89E−07 −2.63 2.63 2.52 227754_at AV700815 0447 “CDNA FLJ10417 fis, 3.93E−07 −2.01 2.01 2.24 clone NT2RP1000112” 226680_at BF056303 0614 Transcribed locus 4.00E−07 −2.17 2.17 2.33 202157_s_at CUGBP2 U69546 0989 “CUG triplet repeat, RNA 4.02E−07 −1.47 1.47 3.3 binding protein 2” 208988_at BE675843 0589 4.05E−07 −1.46 1.46 2.28 222243_s_at TOB2 AB051450 0094 “Transducer of ERBB2, 2” 4.21E−07 −1.35 1.35 2.03 217862_at N24868 0746 Transcribed locus 4.42E−07 1.53 1.53 2.29 64486_at CORO1B AI341234 0185 “Coronin, actin binding 4.42E−07 1.38 1.38 2.35 protein, 1B” 230918_at BE856598 0601 4.43E−07 −1.77 1.77 2.38 204978_at SFRS16 NM_007056 0873 “Splicing factor, 4.48E−07 2.27 2.27 1.8 arginine/serine-rich 16” 232879_at CRTC3 AK024981 0354 CREB regulated 4.61E−07 −2.01 2.01 1.96 transcription coactivator 3 235032_at DNAJA5 BG112118 0672 DnaJ homology subfamily 4.73E−07 −1.89 1.89 2.4 A member 5 203591_s_at CSF3R NM_000760 0761 Colony stimulating factor 3 5.00E−07 2.01 2.01 2.16 receptor (granulocyte) 228098_s_at MYLIP AW292746 0497 Myosin regulatory light 5.00E−07 −1.57 1.57 3.02 chain interacting protein 234734_s_at TNRC6A AK025696 0358 Trinucleotide repeat 5.06E−07 1.67 1.67 2.26 containing 6A 244433_at AI950023 0307 5.36E−07 −2.03 2.03 2.63 226641_at AU157224 0438 “CDNA FLJ11570 fis, 5.42E−07 −1.56 1.56 2.93 clone HEMBA1003309” 222791_at RSBN1 AK022166 0330 Round spermatid basic 5.54E−07 −2.12 2.12 3.08 protein 1 225706_at GLCCI1 AI761989 0259 Glucocorticoid induced 5.60E−07 −1.86 1.86 3 transcript 1 243790_at ZNF585A AA203136 0015 Zinc finger protein 585A 5.73E−07 −2.21 2.21 2.19 244145_at BG260337 0683 5.74E−07 −1.62 1.62 2.4 203751_x_at JUND AI762296 0260 Jun D proto-oncogene 5.89E−07 1.97 1.97 1.9 225216_at CXorf39 AI590719 0220 Chromosome X open 5.91E−07 −1.37 1.37 2.62 reading frame 39 228853_at “(LOC730432, AI652546 0229 Serine/threonine/tyrosine 5.96E−07 −1.49 1.49 2.5 STYX)” interacting protein 232909_s_at “(BPTF, AU146870 0426 “(Bromodomain PHD 6.00E−07 −1.58 1.58 2.89 LOC646043)” finger transcription factor, Similar to Enhancer of bithorax CG32346-PB, isoform B)” 36564_at IBRDC3 W27419 0998 IBR domain containing 3 6.14E−07 1.89 1.89 2.03 200073_s_at HNRPD M94630 0742 “Heterogeneous nuclear 6.30E−07 −1.43 1.43 3.24 ribonucleoprotein D (AU- rich element RNA binding protein 1, 37 kDa)” 200808_s_at ZYX NM_003461 0804 Zyxin 6.30E−07 1.78 1.78 2.6 235125_x_at AI078279 0167 Transcribed locus 6.45E−07 −2.67 2.67 2.17 226712_at BF206389 0627 “CDNA: FLJ22100 fis, 6.45E−07 1.51 1.51 2.3 clone HEP17127” 208447_s_at PRPS1 NM_002764 0795 Phosphoribosyl 6.64E−07 1.93 1.93 1.83 pyrophosphate synthetase 1 226426_at BG149849 0674 Transcribed locus 6.67E−07 −1.5 1.5 2.66 239163_at UBE2B AW364833 0507 Ubiquitin-conjugating 6.80E−07 2.05 2.05 1.81 enzyme E2B (RAD6 homolog) 219426_at EIF2C3 NM_024852 0949 “Eukaryotic translation 6.81E−07 1.65 1.65 1.64 initiation factor 2C, 3” 235341_at LOC144871 AL119957 0387 Hypothetical protein 7.43E−07 1.78 1.78 2.3 LOC144871 242243_at TMF1 AI767435 0264 TATA element modulatory 7.88E−07 −2.26 2.26 2.01 factor 1 201236_s_at BTG2 NM_006763 0870 “BTG family, member 2” 8.07E−07 1.55 1.55 2.45 202577_s_at DDX19A BC005162 0553 DEAD (Asp-Glu-Ala-As) 8.20E−07 −1.44 1.44 2.07 box polypeptide 19A 227772_at AV700849 0448 9.74E−07 −1.72 1.72 2.33 229897_at ZNF641 BF195808 0626 Zinc finger protein 641 9.75E−07 1.86 1.86 2.15 218566_s_at CHORDC1 NM_012124 0876 Cysteine and histidine-rich 9.81E−07 −1.61 1.61 2.33 domain (CHORD)- containing 1 203839_s_at TNK2 NM_005781 0845 “Tyrosine kinase, non- 9.95E−07 2.11 2.11 1.63 receptor, 2” 204361_s_at SKAP2 AB014486 0085 Src kinase associated 1.02E−06 −1.79 1.79 2.09 phosphoprotein 2 224250_s_at SECISBP2 BC001189 0541 SECIS binding protein 2 1.02E−06 1.74 1.74 2.57 225350_s_at ZYG11B AV701229 0449 Zyg-11 homolog B (C. elegans) 1.03E−06 −1.54 1.54 2.83 204516_at BG390306 0692 Transcribed locus 1.05E−06 −2.17 2.17 2.56 225620_at RAB35 AL534848 0412 “RAB35, member RAS 1.05E−06 1.56 1.56 2.27 oncogene family” 226965_at FAM116A BF438017 0636 “(Family with sequence 1.07E−06 −1.53 1.53 2.91 similarity 116, member A, Transcribed locus)” 239808_at AI084489 0169 Transcribed locus 1.08E−06 −1.87 1.87 2.47 227428_at GABPA BE876628 0605 “GA binding protein 1.20E−06 −1.53 1.53 2.52 transcription factor, alpha subunit 60 kDa” 218595_s_at “(HEATR1, NM_018072 0921 “Lectin, galactoside- 1.20E−06 −1.43 1.43 2.3 LGALS8)” binding, soluble, 8 (galectin 8)” 222266_at C19orf2 BF796940 0661 Chromosome 19 open 1.23E−06 −1.72 1.72 2.17 reading frame 2 239597_at AA993566 0080 1.23E−06 2.33 2.33 2.06 203415_at PDCD6 NM_013232 0879 Programmed cell death 6 1.23E−06 1.36 1.36 2.2 208866_at BF510713 0642 CDNA clone 1.23E−06 −1.59 1.59 2.2 IMAGE: 4044084 212575_at C19orf6 BF966155 0665 Chromosome 19 open 1.27E−06 12.23 12.23 0.38 reading frame 6 225176_at AA156754 0013 “CDNA FLJ42149 fis, 1.30E−06 −1.4 1.4 2.96 clone THYMU1000692” 227223_at RBM39 BE466173 0575 RNA binding motif protein 1.32E−06 2.29 2.29 2.22 39 41386_i_at JMJD3 AB002344 0082 Jumonji domain 1.33E−06 1.7 1.7 2.35 containing 3 225995_x_at “(FAM39DP, BG178695 0675 “(CXYorf1-related protein, 1.38E−06 1.64 1.64 2.45 FLJ00038, Family with sequence LOC376475, similarity 39, member D LOC727741)” pseudogene)” 228328_at KLHL28 AI982758 0311 Kelch-like 28 (Drosophila) 1.41E−06 −1.71 1.71 2.43 235409_at MGA AU149225 0429 MAX gene associated 1.41E−06 2.4 2.4 1.89 200649_at NUCB1 BC002356 0544 Nucleobindin 1 1.42E−06 1.85 1.85 2.2 232615_at AA632758 0034 Transcribed locus 1.43E−06 −2.01 2.01 3.06 205882_x_at ADD3 AI818488 0278 Adducin 3 (gamma) 1.44E−06 −1.46 1.46 3.28 228496_s_at CRIM1 AW243081 0489 Cysteine rich 1.44E−06 −2.14 2.14 2.18 transmembrane BMP regulator 1 (chordin-like) 209189_at FOS BC004490 0549 V-fos FBJ murine 1.50E−06 3.42 3.42 2.61 osteosarcoma viral oncogene homolog 239233_at KIAA1212 AA744613 0053 KIAA1212 1.53E−06 −2.29 2.29 1.4 224308_s_at INTS2 AL136800 0393 Integrator complex subunit 2 1.61E−06 −1.98 1.98 1.98 208705_s_at EIF5 BG481972 0696 Eukaryotic translation 1.62E−06 1.3 1.3 2.56 initiation factor 5 218607_s_at SDAD1 NM_018115 0922 SDA1 domain containing 1 1.63E−06 1.52 1.52 2.24 200041_s_at BAT1 NM_004640 0826 HLA-B associated 1.71E−06 1.29 1.29 2.94 transcript 1 202850_at ABCD3 NM_002858 0796 “ATP-binding cassette, 1.71E−06 −1.56 1.56 2.3 sub-family D (ALD), member 3” 224562_at “(LOC644739, AK025566 0357 “(Similar to Wiskott- 1.73E−06 1.76 1.76 2.94 LOC647909, Aldrich syndrome protein WASF2)” family member 4 (WASP- family protein member 4), WAS protein family, member 2)” 222644_s_at GLT25D1 AI924150 0296 Glycosyltransferase 25 1.80E−06 2.01 2.01 2.09 domain containing 1 212536_at ATP11B AB023173 0088 “ATPase, Class VI, type 1.81E−06 −1.52 1.52 2.17 11B” 215269_at TMEM1 AI922538 0294 Transmembrane protein 1 1.82E−06 −1.96 1.96 2.01 243303_at AA811657 0064 1.93E−06 −1.92 1.92 2.34 201991_s_at KIF5B BF223224 0630 Kinesin family member 5B 1.95E−06 −1.36 1.36 2.75 213327_s_at USP12 AI820101 0280 Ubiquitin specific 1.97E−06 −1.58 1.58 1.97 peptidase 12 213882_at TM2D1 AA012917 0001 TM2 domain containing 1 1.97E−06 −1.68 1.68 1.66 214715_x_at ZNF160 AK024789 0348 Zinc finger protein 160 2.00E−06 −1.65 1.65 2.37 225845_at ZBTB44 BG253884 0681 Zinc finger and BTB 2.01E−06 −1.68 1.68 2.81 domain containing 44 215529_x_at DIP2A AI590053 0219 DIP2 disco-interacting 2.01E−06 −1.99 1.99 1.89 protein 2 homolog A (Drosophila) 242539_at LOC730069 AW665509 0523 Similar to nuclear receptor 2.04E−06 −2.21 2.21 2.33 binding factor 2 203311_s_at ARF6 M57763 0735 ADP-ribosylation factor 6 2.07E−06 1.9 1.9 2.23 205854_at TULP3 AK024246 0342 Tubby like protein 3 2.08E−06 −1.57 1.57 1.79 212042_x_at “(LOC653949, BG389744 0691 Ribosomal protein L7 2.10E−06 −1.37 1.37 3.51 RPL7, hCG_2015956, hCG_31916)” 233369_at AU146027 0424 “CDNA FLJ11835 fis, 2.23E−06 −1.78 1.78 2.42 clone HEMBA1006595” 212513_s_at USP33 AB029020 0089 Ubiquitin specific 2.27E−06 −1.31 1.31 2.52 peptidase 33 218626_at EIF4ENIF1 NM_019843 0930 Eukaryotic translation 2.30E−06 −1.33 1.33 2.1 initiation factor 4E nuclear import factor 1 208246_x_at NM_017618 0909 2.31E−06 −1.63 1.63 2.29 224559_at MALAT1 AF001540 0104 Metastasis associated 2.36E−06 4.55 4.55 2.49 lung adenocarcinoma transcript 1 (non-coding RNA) 205312_at SPI1 NM_003120 0798 Spleen focus forming virus 2.41E−06 2.77 2.77 1.91 (SFFV) proviral integration oncogene spi1 213318_s_at BAT3 BG028844 0669 HLA-B associated 2.45E−06 1.41 1.41 2.56 transcript 3 212099_at RHOB AI263909 0179 “Ras homolog gene 2.50E−06 2.36 2.36 2.32 family, member B” 223131_s_at TRIM8 AI925572 0299 Tripartite motif-containing 8 2.51E−06 1.74 1.74 1.9 212487_at GPATCH8 AI673812 0234 G patch domain 2.53E−06 2.33 2.33 1.57 containing 8 200011_s_at ARF3 NM_001659 0775 ADP-ribosylation factor 3 2.55E−06 1.43 1.43 2.95 210543_s_at “(LOC731751, U34994 0981 “Protein kinase, DNA- 2.61E−06 −1.39 1.39 2.21 PRKDC)” activated, catalytic polypeptide” 217313_at AC004692 0098 2.63E−06 −1.62 1.62 2.34 228106_at C4orf30 AA031528 0004 Chromosome 4 open 2.66E−06 −1.57 1.57 2.42 reading frame 30 218043_s_at AZI2 NM_022461 0940 5-azacytidine induced 2 2.67E−06 −2.08 2.08 1.89 203514_at MAP3K3 BF971923 0666 Mitogen-activated protein 2.67E−06 −1.52 1.52 2.21 kinase kinase kinase 3 223295_s_at LUC7L BE049621 0566 LUC7-like (S. cerevisiae) 2.68E−06 −1.57 1.57 2.67 235469_at MGC40405 AV744101 0457 Hypothetical protein 2.73E−06 −2.48 2.48 1.95 MGC40405 209440_at PRPS1 BC001605 0542 Phosphoribosyl 2.77E−06 1.42 1.42 2.22 pyrophosphate synthetase 1 227039_at AKAP13 AI674926 0235 A kinase (PRKA) anchor 2.82E−06 1.92 1.92 2.46 protein 13 218499_at RP6-213H19.1 NM_016542 0904 Serine/threonine protein 2.94E−06 −1.52 1.52 2.53 kinase MST4 232440_at ZDHHC13 AU155198 0433 “Zinc finger, DHHC-type 2.95E−06 −1.75 1.75 2.26 containing 13” 209727_at GM2A M76477 0737 GM2 ganglioside activator 2.97E−06 5.7 5.7 1.01 241891_at T92908 0972 2.97E−06 −1.82 1.82 2.64 227525_at GLCCI1 AA058770 0006 Glucocorticoid induced 3.10E−06 −1.75 1.75 2.66 transcript 1 228088_at AI092265 0170 “CDNA FLJ31513 fis, 3.17E−06 −1.49 1.49 2.11 clone NT2RI1000127” 242362_at AI797788 0269 3.17E−06 −2.27 2.27 2.69 34478_at RAB11B X79780 1009 “RAB11B, member RAS 3.23E−06 2.63 2.63 1.27 oncogene family” 223135_s_at BBX AL136769 0392 Bobby sox homolog 3.25E−06 1.41 1.41 2.47 (Drosophila) 225780_at RSC1A1 AL565415 0418 “Regulatory solute carrier 3.26E−06 −1.59 1.59 2.5 protein, family 1, member 1” 211791_s_at KCNAB2 AF044253 0112 “Potassium voltage-gated 3.27E−06 4.73 4.73 1.31 channel, shaker-related subfamily, beta member 2” 204252_at CDK2 M68520 0736 Cyclin-dependent kinase 2 3.29E−06 −1.38 1.38 2.06 202420_s_at DHX9 NM_001357 0771 DEAH (Asp-Glu-Ala-His) 3.31E−06 −1.29 1.29 2.35 box polypeptide 9 223138_s_at DHX36 AI937206 0304 DEAH (Asp-Glu-Ala-His) 3.31E−06 1.69 1.69 2.21 box polypeptide 36 240452_at GSPT1 AA580082 0030 G1 to S phase transition 1 3.38E−06 −2.24 2.24 2.5 202082_s_at SEC14L1 AV748469 0458 SEC14-like 1 (S. cerevisiae) 3.38E−06 1.72 1.72 1.74 213038_at IBRDC3 AL031602 0365 IBR domain containing 3 3.63E−06 1.55 1.55 1.95 232038_at C6orf170 AI052103 0162 Chromosome 6 open 3.76E−06 −2 2 1.73 reading frame 170 229036_at TNRC6B AI681177 0238 “(Transcribed locus, 3.80E−06 1.83 1.83 2.32 Trinucleotide repeat containing 6B)” 229235_at AI983432 0312 Transcribed locus 3.81E−06 −1.53 1.53 2.59 226412_at C6orf111 N66397 0752 Chromosome 6 open 3.84E−06 −1.63 1.63 2.76 reading frame 111 212637_s_at WWP1 AU155187 0432 WW domain containing E3 3.95E−06 −1.64 1.64 1.62 ubiquitin protein ligase 1 220296_at NM_024564 0947 3.99E−06 −1.96 1.96 2 240695_at AA876138 0075 4.03E−06 1.68 1.68 1.78 224759_s_at C12orf23 AK001731 0320 Chromosome 12 open 4.20E−06 −1.63 1.63 2.48 reading frame 23 222794_x_at PAPD1 AK022188 0331 PAP associated domain 4.32E−06 −1.41 1.41 2.51 containing 1 224974_at SUDS3 AK024460 0344 Suppressor of defective 4.36E−06 −1.94 1.94 2.27 silencing 3 homolog (S. cerevisiae) 242650_at AW298590 0503 Transcribed locus 4.42E−06 −2.21 2.21 1.84 212921_at SMYD2 AF070592 0121 SET and MYND domain 4.45E−06 −1.74 1.74 1.88 containing 2 217717_s_at YWHAB BF246499 0631 “Tyrosine 3- 4.47E−06 1.58 1.58 2.51 monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide” 221419_s_at NM_013307 0880 4.56E−06 2.08 2.08 2.03 204809_at CLPX NM_006660 0866 ClpX caseinolytic 4.61E−06 −1.37 1.37 1.99 peptidase X homolog (E. coli) 201409_s_at PPP1CB NM_002709 0794 “Protein phosphatase 1, 4.64E−06 −1.38 1.38 2.43 catalytic subunit, beta isoform” 209829_at C6orf32 AB002384 0083 Chromosome 6 open 4.67E−06 −1.61 1.61 2.89 reading frame 32 225761_at PAPD4 AI434509 0203 PAP associated domain 4.74E−06 −1.42 1.42 2.78 containing 4 228471_at ANKRD44 AA744636 0054 Ankyrin repeat domain 44 4.84E−06 −1.71 1.71 2.75 201526_at ARF5 NM_001662 0776 ADP-ribosylation factor 5 4.87E−06 1.49 1.49 2.21 241435_at AA702930 0044 5.03E−06 −2.16 2.16 3.23 227567_at AMZ2 AL524467 0407 Archaemetzincins-2 5.11E−06 −1.69 1.69 2.53 209563_x_at CALM1 BC000454 0537 “Calmodulin 1 5.22E−06 1.68 1.68 2.84 (phosphorylase kinase, delta)” 242518_at AA748423 0056 5.26E−06 1.6 1.6 1.87 239049_at BF514509 0644 5.31E−06 −1.85 1.85 2.38 209024_s_at SYNCRIP AI472757 0209 “Synaptotagmin binding, 5.50E−06 1.48 1.48 2.14 cytoplasmic RNA interacting protein” 211948_x_at BAT2D1 BG261071 0685 BAT2 domain containing 1 5.57E−06 2.77 2.77 2.01 228446_at KIAA2026 BF062203 0616 KIAA2026 5.67E−06 −1.44 1.44 2.53 229541_at BE669703 0583 “CDNA FLJ38918 fis, 5.86E−06 1.96 1.96 1.97 clone NT2NE2010633” 237330_at AA603494 0033 Transcribed locus 5.89E−06 −2.48 2.48 1.96 217842_at LUC7L2 NM_016019 0893 LUC7-like 2 (S. cerevisiae) 5.90E−06 −1.51 1.51 1.79 201828_x_at FAM127A NM_003928 0809 “Family with sequence 5.96E−06 1.27 1.27 2.33 similarity 127, member A” 229366_at BG149765 0673 Transcribed locus 5.98E−06 −1.33 1.33 2.34 201986_at THRAP1 AB011165 0084 Thyroid hormone receptor 6.02E−06 −1.46 1.46 2.51 associated protein 1 202373_s_at RAB3GAP2 AF255648 0148 RAB3 GTPase activating 6.03E−06 −1.34 1.34 2.46 protein subunit 2 (non- catalytic) 241906_at BF001773 0612 6.07E−06 −2.1 2.1 2.45 201318_s_at “(MRCL3, NM_006471 0863 “(Myosin regulatory light 6.16E−06 −1.33 1.33 3.25 MRLC2)” chain MRCL3, Myosin regulatory light chain MRLC2)” 207941_s_at RBM39 NM_004902 0830 RNA binding motif protein 6.17E−06 −1.34 1.34 2.85 39 229586_at CHD9 AW300405 0505 Chromodomain helicase 6.33E−06 1.64 1.64 2.01 DNA binding protein 9 217336_at AL118510 0385 6.34E−06 −1.68 1.68 2.28 209648_x_at SOCS5 AL136896 0394 Suppressor of cytokine 6.36E−06 −1.86 1.86 1.59 signaling 5 226664_at TBC1D20 AL121747 0388 “TBC1 domain family, 6.40E−06 1.39 1.39 2.3 member 20” 225786_at LOC284702 AI440495 0204 Hypothetical protein 6.49E−06 −1.6 1.6 2.45 LOC284702 208635_x_at NACA BF976260 0667 Nascent-polypeptide- 6.53E−06 −1.24 1.24 3.71 associated complex alpha polypeptide 223444_at SENP7 AL136599 0391 SUMO1/sentrin specific 6.56E−06 −1.88 1.88 2.36 peptidase 7 208975_s_at KPNB1 L38951 0725 Karyopherin (importin) 6.58E−06 −1.54 1.54 2.17 beta 1 208935_s_at LGALS8 L78132 0727 “Lectin, galactoside- 6.59E−06 −1.66 1.66 2.18 binding, soluble, 8 (galectin 8)” 200847_s_at TMEM66 NM_016127 0895 Transmembrane protein 6.65E−06 −1.29 1.29 3.1 66 218247_s_at RKHD2 NM_016626 0906 Ring finger and KH 6.67E−06 −1.93 1.93 2.32 domain containing 2 227121_at BF476076 0640 MRNA; cDNA 6.71E−06 −1.51 1.51 2.61 DKFZp586K1922 (from clone DKFZp586K1922) 235984_at AL036662 0367 Transcribed locus 6.72E−06 1.85 1.85 2 212069_s_at KIAA0515 AK026025 0360 KIAA0515 6.72E−06 1.73 1.73 1.89 243649_at AI678692 0236 6.73E−06 −1.82 1.82 2.15 238549_at AI420611 0201 Transcribed locus 6.84E−06 −1.43 1.43 2.5 233093_s_at BIRC6 AK023788 0339 Baculoviral IAP repeat- 6.88E−06 −1.25 1.25 2.93 containing 6 (apollon) 221749_at YTHDF3 AU157915 0439 “YTH domain family, 6.98E−06 −1.61 1.61 2.37 member 3” 242726_at BF221850 0629 Transcribed locus 7.03E−06 −2 2 2.11 242195_x_at NUMBL BE350811 0573 Numb homolog 7.11E−06 −1.48 1.48 2.77 (Drosophila)-like 204020_at PURA BF739943 0658 Purine-rich element 7.23E−06 −1.4 1.4 2.5 binding protein A 208694_at PRKDC U47077 0984 “Protein kinase, DNA- 7.38E−06 −1.5 1.5 2.12 activated, catalytic polypeptide” 200047_s_at YY1 NM_003403 0802 YY1 transcription factor 7.42E−06 −1.29 1.29 2.83 228097_at MYLIP AW292746 0497 Myosin regulatory light 7.43E−06 −1.57 1.57 2.55 chain interacting protein 213605_s_at AL049987 0376 MRNA; cDNA 7.49E−06 −2.47 2.47 2.16 DKFZp564F112 (from clone DKFZp564F112) 218259_at MKL2 NM_014048 0881 MKL/myocardin-like 2 7.81E−06 −1.57 1.57 2.02 240338_at LRAP AI807341 0272 Leukocyte-derived 7.89E−06 −2.06 2.06 1.76 arginine aminopeptidase 226366_at SHPRH AI828221 0285 SNF2 histone linker PHD 7.99E−06 −1.32 1.32 2.24 RING helicase 218237_s_at SLC38A1 NM_030674 0955 “Solute carrier family 38, 8.02E−06 −1.91 1.91 2.93 member 1” 201473_at JUNB NM_002229 0783 Jun B proto-oncogene 8.04E−06 1.97 1.97 2.54 226786_at RFX1 BF507952 0641 “Regulatory factor X, 1 8.06E−06 1.46 1.46 2.56 (influences HLA class II expression)” 214948_s_at AL050136 0377 MRNA; cDNA 8.09E−06 −1.4 1.4 2.26 DKFZp586L141 (from clone DKFZp586L141) 225672_at GOLGA2 AL514295 0405 “Golgi autoantigen, golgin 8.22E−06 1.32 1.32 2.53 subfamily a, 2” 229787_s_at OGT AI742039 0251 O-linked N- 8.27E−06 −2.15 2.15 2.41 acetylglucosamine (GlcNAc) transferase (UDP-N- acetylglucosamine:polypeptide- N- acetylglucosaminyl transferase) 202253_s_at DNM2 NM_004945 0832 Dynamin 2 8.34E−06 1.63 1.63 1.93 225564_at SPATA13 AW269397 0493 Spermatogenesis 8.50E−06 −1.7 1.7 2.97 associated 13 218967_s_at PTER NM_030664 0954 Phosphotriesterase 8.54E−06 −1.53 1.53 2.11 related 217007_s_at ADAM15 AK000667 0316 ADAM metallopeptidase 8.61E−06 4.58 4.58 0.88 domain 15 (metargidin) 228250_at FNIP1 AW263086 0491 Folliculin interacting 8.65E−06 2.39 2.39 1.78 protein 1 212291_at HIPK1 AI393355 0199 Homeodomain interacting 8.65E−06 1.96 1.96 2.07 protein kinase 1 203203_s_at KRR1 NM_007043 0872 “KRR1, small subunit 8.67E−06 −1.64 1.64 1.93 (SSU) processome component, homolog (yeast)” 229470_at FAM105B AW451634 0509 “Family with sequence 8.88E−06 −1.53 1.53 2.41 similarity 105, member B” 224698_at FAM62B AB033054 0090 Family with sequence 8.90E−06 −1.58 1.58 2.83 similarity 62 (C2 domain containing) member B 244061_at AI510829 0213 8.91E−06 −2.35 2.35 2.44 204075_s_at KIAA0562 NM_014704 0887 KIAA0562 9.05E−06 −2.13 2.13 1.39 217019_at AL137162 0395 9.06E−06 −2.35 2.35 1.82 218600_at LIMD2 NM_030576 0953 LIM domain containing 2 9.07E−06 1.85 1.85 2.01 213606_s_at ARHGDIA AI571798 0218 Rho GDP dissociation 9.08E−06 2.93 2.93 1.41 inhibitor (GDI) alpha 201260_s_at SYPL1 NM_006754 0869 Synaptophysin-like 1 9.26E−06 −1.5 1.5 2.48 234340_at AK021431 0324 “CDNA FLJ11369 fis, 9.44E−06 −1.75 1.75 1.7 clone HEMBA1000338” 207686_s_at CASP8 NM_001228 0770 “Caspase 8, apoptosis- 9.51E−06 2.19 2.19 1.79 related cysteine peptidase” 201332_s_at STAT6 NM_003153 0799 “Signal transducer and 9.57E−06 1.49 1.49 2.01 activator of transcription 6, interleukin-4 induced” 203388_at ARRB2 NM_004313 0819 “Arrestin, beta 2” 9.59E−06 1.54 1.54 2.66 204275_at SOLH AI796687 0268 Small optic lobes homolog 9.61E−06 1.51 1.51 1.72 (Drosophila) 238057_at USP45 AW195800 0487 Ubiquitin specific 9.61E−06 −2.28 2.28 1.91 peptidase 45 242352_at NIPBL AW272262 0494 Nipped-B homolog 9.63E−06 2.68 2.68 1.78 (Drosophila) 212846_at RRP1B AA811192 0063 KIAA0179 9.81E−06 −1.28 1.28 2.51 212090_at GRINA AL571424 0420 “Glutamate receptor, 9.90E−06 1.94 1.94 1.99 ionotropic, N-methyl D- asparate-associated protein 1 (glutamate binding)” 227636_at THAP5 BG500677 0698 THAP domain containing 5 9.92E−06 −1.73 1.73 2.29 209379_s_at KIAA1128 AF241785 0147 KIAA1128 9.94E−06 −1.5 1.5 2.33 230180_at AA521056 0025 9.99E−06 2.56 2.56 1.96 217489_s_at IL6R S72848 0968 Interleukin 6 receptor 1.01E−05 2.12 2.12 1.44 200014_s_at “(HNRPC, NM_004500 0824 Heterogeneous nuclear 1.03E−05 −1.21 1.21 2.71 hCG_1641229)” ribonucleoprotein C (C1/C2) 221628_s_at N-PAC AF326966 0155 Cytokine-like nuclear 1.03E−05 2.06 2.06 1.63 factor n-pac 214594_x_at ATP8B1 BG252666 0680 “ATPase, Class I, type 8B, 1.05E−05 −2.44 2.44 2.17 member 1” 218528_s_at RNF38 NM_022781 0941 Ring finger protein 38 1.05E−05 −1.27 1.27 2.49 223494_at MGEA5 AF307332 0152 Meningioma expressed 1.08E−05 −1.49 1.49 3.22 antigen 5 (hyaluronidase) 234260_at AL122039 0390 MRNA; cDNA 1.09E−05 −2.06 2.06 1.99 DKFZp434E0572 (from clone DKFZp434E0572) 203104_at CSF1R NM_005211 0838 “Colony stimulating factor 1.09E−05 1.96 1.96 2.55 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog” 221755_at EHBP1L1 BG334196 0688 EH domain binding protein 1.10E−05 1.88 1.88 1.68 1-like 1 200976_s_at TAX1BP1 NM_006024 0850 Tax1 (human T-cell 1.11E−05 −1.26 1.26 2.84 leukemia virus type I) binding protein 1 212297_at ATP13A3 BF218804 0628 ATPase type 13A3 1.12E−05 −1.73 1.73 2 208841_s_at G3BP2 AB014560 0086 GTPase activating protein 1.12E−05 −1.37 1.37 2.55 (SH3 domain) binding protein 2 200632_s_at NDRG1 NM_006096 0853 N-myc downstream 1.13E−05 1.38 1.38 2.35 regulated gene 1 215383_x_at SPG21 AL137312 0397 “Spastic paraplegia 21, 1.13E−05 −1.61 1.61 2.29 maspardin (autosomal recessive, Mast syndrome)” 235493_at AI927329 0300 Transcribed locus 1.15E−05 −1.86 1.86 2.33 236614_at LOC729683 AW006288 0463 Hypothetical protein 1.15E−05 1.36 1.36 2.25 LOC729683 209273_s_at ISCA1 BG387555 0690 Iron-sulfur cluster 1.16E−05 −1.44 1.44 2.16 assembly 1 homolog (S. cerevisiae) 227621_at WTAP BE464729 0574 Wilms tumor 1 associated 1.18E−05 −1.37 1.37 3.2 protein 225431_x_at ACY1L2 BE779764 0596 Aminoacylase 1-like 2 1.18E−05 −2.17 2.17 2.43 235879_at AI697540 0245 Transcribed locus 1.20E−05 −2.13 2.13 2.94 226825_s_at TMEM165 AW665624 0524 Transmembrane protein 1.22E−05 1.67 1.67 2.76 165 218143_s_at SCAMP2 NM_005697 0843 Secretory carrier 1.22E−05 1.46 1.46 2.38 membrane protein 2 203890_s_at DAPK3 BF686824 0655 Death-associated protein 1.24E−05 1.7 1.7 1.41 kinase 3 208313_s_at SF1 NM_004630 0825 Splicing factor 1 1.27E−05 1.4 1.4 2.67 211352_s_at NCOA3 U80737 0991 Nuclear receptor 1.28E−05 1.88 1.88 1.74 coactivator 3 224579_at SLC38A1 BF247552 0632 “Solute carrier family 38, 1.28E−05 −1.46 1.46 3.14 member 1” 201752_s_at ADD3 AI763123 0262 Adducin 3 (gamma) 1.28E−05 −1.44 1.44 3.26 231747_at CYSLTR1 NM_006639 0864 Cysteinyl leukotriene 1.30E−05 1.73 1.73 2.57 receptor 1 208319_s_at RBM3 NM_006743 0868 “RNA binding motif 1.30E−05 −1.66 1.66 2.61 (RNP1, RRM) protein 3” 227159_at GHDC AI827015 0284 GH3 domain containing 1.33E−05 1.45 1.45 2.3 230387_at AL038450 0371 Transcribed locus 1.33E−05 −1.75 1.75 2.34

TABLE 2B Known Genbank SEQ Mean Signal Log10 Mean Top 42 Fragment Genes: Gene Accession ID Sequence Clusters: Control Mean (MS Signal MS (FC Name Symbol No. NO. Cluster Title Samples Samples) Samples Filtered) 214847_s_at GPSM3 BG111168 0671 “G-protein signalling 158.4893192 2.46 288.4031503 modulator 3 (AGS3-like, C. elegans)” 227510_x_at AL037917 0369 Transcribed locus 194.98446 3.09 1230.268771 1 223578_x_at MALAT1 AF113016 0131 Metastasis associated 67.60829754 2.36 229.0867653 2 lung adenocarcinoma transcript 1 (non-coding RNA) 232431_at AI934556 0302 “Glucocorticoid receptor 331.1311215 2.08 120.2264435 3 alpha mRNA, variant 3′ UTR” 219878_s_at KLF13 NM_015995 0892 Kruppel-like factor 13 2.511886432 1.53 33.88441561 4 214352_s_at KRAS BF673699 0652 V-Ki-ras2 Kirsten rat 114.8153621 2.41 257.0395783 5 sarcoma viral oncogene homolog 228582_x_at MALAT1 AI475544 0211 Metastasis associated 245.4708916 3.37 2344.228815 6 lung adenocarcinoma transcript 1 (non-coding RNA) 243981_at AI763206 0263 Transcribed locus 316.227766 2.12 131.8256739 7 201753_s_at ADD3 NM_019903 0931 Adducin 3 (gamma) 1445.439771 2.89 776.2471166 211074_at FOLR1 AF000381 0102 Folate receptor 1 (adult) 144.5439771 2.54 346.7368505 8 225956_at LOC153222 AL565238 0417 Adult retina protein 741.3102413 2.7 501.1872336 223161_at KIAA1147 AA029331 0003 KIAA1147 186.2087137 2.63 426.5795188 9 218389_s_at APH1A NM_016022 0894 Anterior pharynx defective 181.9700859 2.44 275.4228703 1 homolog A (C. elegans) 236924_at GLMN AA814383 0065 “Glomulin, FKBP 112.2018454 1.66 45.70881896 10 associated protein” 226148_at ZBTB44 AU144305 0422 Zinc finger and BTB 912.0108394 2.71 512.861384 domain containing 44 219696_at FLJ20054 NM_019049 0927 Hypothetical protein 151.3561248 2.02 104.7128548 FLJ20054 223940_x_at AF132202 0134 281.8382931 2.92 831.7637711 11 225889_at AEBP2 BF475280 0639 AE binding protein 2 489.7788194 2.41 257.0395783 214697_s_at ROD1 AW190873 0485 ROD1 regulator of 79.43282347 2.26 181.9700859 12 differentiation 1 (S. pombe) 208610_s_at SRRM2 AI655799 0233 Serine/arginine repetitive 52.48074602 2.22 165.9586907 13 matrix 2 241751_at OFD1 AW292752 0498 Oral-facial-digital 147.9108388 1.79 61.65950019 14 syndrome 1 204049_s_at PHACTR2 NM_014721 0889 Phosphatase and actin 213.796209 2.1 125.8925412 regulator 2 225377_at C9orf86 BE783949 0597 Chromosome 9 open 186.2087137 2.55 354.8133892 reading frame 86 225139_at RBM35B AW070424 0473 RNA binding motif protein 1000 2.8 630.9573445 35B 216177_at LOC391132 AW582267 0519 Similar to 60S ribosomal 154.8816619 1.92 83.17637711 protein L29 (P23) 242232_at AI652864 0232 50.11872336 2.03 107.1519305 15 200734_s_at ARF3 BG341906 0689 ADP-ribosylation factor 3 177.827941 2.5 316.227766 211716_x_at ARHGDIA BC005851 0554 Rho GDP dissociation 416.8693835 2.84 691.8309709 inhibitor (GDI) alpha 215460_x_at BRD1 AL080149 0380 Bromodomain containing 1 177.827941 2.11 128.8249552 222576_s_at EIF2C1 AW071829 0475 “Eukaryotic translation 138.0384265 2.42 263.0267992 initiation factor 2C, 1” 230141_at ARID4A AI640594 0226 AT rich interactive domain 154.8816619 1.92 83.17637711 4A (RBP1-like) 227740_at UHMK1 AW173222 0481 U2AF homology motif 234.4228815 2.76 575.4399373 16 (UHM) kinase 1 204805_s_at H1FX NM_006026 0851 “H1 histone family, 181.9700859 2.63 426.5795188 17 member X” 208624_s_at EIF4G1 BE966878 0610 “Eukaryotic translation 75.8577575 2.03 107.1519305 initiation factor 4 gamma, 1” 243612_at NSD1 AL526448 0408 Nuclear receptor binding 154.8816619 1.77 58.88436554 18 SET domain protein 1 201167_x_at ARHGDIA D13989 0704 Rho GDP dissociation 52.48074602 2.11 128.8249552 19 inhibitor (GDI) alpha 241786_at AI380514 0198 Transcribed locus 407.3802778 2.25 177.827941 20 238430_x_at SLFN5 AI923675 0295 Schlafen family member 5 371.5352291 3 1000 21 202102_s_at BRD4 BF718610 0657 Bromodomain containing 4 208.9296131 2.51 323.5936569 201737_s_at MARCH6 NM_005885 0847 Membrane-associated 338.8441561 2.28 190.5460718 ring finger (C3HC4) 6 229926_at AI633738 0225 Transcribed locus 109.6478196 1.83 67.60829754 230961_at BE856980 0603 117.4897555 1.76 57.54399373 22 201996_s_at SPEN AL524033 0406 “Spen homolog, 35.48133892 1.96 91.20108394 23 transcriptional regulator (Drosophila)” 231858_x_at DKFZp761E198 BC004895 0552 DKFZp761E198 protein 104.7128548 2.28 190.5460718 200608_s_at RAD21 NM_006265 0855 RAD21 homolog (S. pombe) 407.3802778 2.45 281.8382931 201168_x_at ARHGDIA NM_004309 0818 Rho GDP dissociation 234.4228815 2.63 426.5795188 inhibitor (GDI) alpha 224631_at ZFP91 AA758013 0058 Zinc finger protein 91 104.7128548 2.31 204.1737945 homolog (mouse) 225563_at PAN3 AI970788 0309 PAN3 polyA specific 1071.519305 2.82 660.693448 ribonuclease subunit homolog (S. cerevisiae) 222133_s_at PHF20L1 AK022280 0332 PHD finger protein 20-like 1 131.8256739 1.91 81.28305162 237768_x_at AA825925 0066 371.5352291 2.21 162.1810097 24 208677_s_at BSG AL550657 0415 Basigin (Ok blood group) 83.17637711 2.27 186.2087137 25 224572_s_at IRF2BP2 BG485163 0697 Interferon regulatory factor 426.5795188 3 1000 26 2 binding protein 2 221899_at PFAAP5 AI809961 0274 Phosphonoformate 316.227766 2.22 165.9586907 immuno-associated protein 5 224969_at ATXN7L3 AL390158 0401 Ataxin 7-like 3 208.9296131 2.54 346.7368505 229389_at ATG16L2 AA741058 0050 ATG16 autophagy related 208.9296131 2.8 630.9573445 27 16-like 2 (S. cerevisiae) 242134_at AI733194 0247 Transcribed locus 52.48074602 2.06 114.8153621 28 224676_at TMED4 AI472339 0208 Transmembrane emp24 281.8382931 2.77 588.8436554 29 protein transport domain containing 4 224568_x_at MALAT1 AW005982 0462 Metastasis associated 190.5460718 2.78 602.5595861 30 lung adenocarcinoma transcript 1 (non-coding RNA) 218659_at ASXL2 NM_018263 0923 Additional sex combs like 758.577575 2.72 524.8074602 2 (Drosophila) 203497_at PPARBP NM_004774 0829 PPAR binding protein 251.1886432 2.21 162.1810097 204285_s_at PMAIP1 AI857639 0289 Phorbol-12-myristate-13- 66.0693448 2.23 169.8243652 31 acetate-induced protein 1 213015_at BF448315 0638 “ARTC1 mRNA, complete 89.12509381 2.35 223.8721139 32 sequence” 224567_x_at MALAT1 BG534952 0699 Metastasis associated 295.1209227 2.91 812.8305162 33 lung adenocarcinoma transcript 1 (non-coding RNA) 222790_s_at RSBN1 AK022166 0330 Round spermatid basic 741.3102413 2.53 338.8441561 34 protein 1 207057_at SLC16A7 NM_004731 0828 “Solute carrier family 16, 25.70395783 2.01 102.3292992 35 member 7 (monocarboxylic acid transporter 2)” 212852_s_at TROVE2 AL538601 0414 “TROVE domain family, 407.3802778 2.46 288.4031503 member 2” 238761_at BE645241 0581 724.4359601 2.46 288.4031503 36 214198_s_at DGCR2 AU150824 0430 DiGeorge syndrome 177.827941 2.03 107.1519305 critical region gene 2 202809_s_at INTS3 NM_023015 0943 Integrator complex subunit 3 154.8816619 2.09 123.0268771 236072_at N64578 0751 Transcribed locus 81.28305162 1.54 34.67368505 37 225827_at EIF2C2 AI832074 0288 “Eukaryotic translation 138.0384265 2.54 346.7368505 38 initiation factor 2C, 2” 241775_at AW298119 0502 “CDNA FLJ26437 fis, 316.227766 2.16 144.5439771 39 clone KDN02067” 215706_x_at ZYX BC002323 0543 Zyxin 398.1071706 2.83 676.0829754 201730_s_at TPR BF110993 0619 Translocated promoter 194.98446 2.54 346.7368505 region (to activated MET oncogene) 226447_at ASH1L BG290742 0687 “Ash1 (absent, small, or 398.1071706 2.42 263.0267992 homeotic)-like (Drosophila)” 200623_s_at CALM3 NM_005184 0836 “Calmodulin 3 213.796209 2.6 398.1071706 (phosphorylase kinase, delta)” 215990_s_at BCL6 S67779 0966 B-cell CLL/lymphoma 6 63.09573445 2.1 125.8925412 (zinc finger protein 51) 212007_at UBXD2 AI927512 0301 UBX domain containing 2 112.2018454 2.23 169.8243652 225885_at EEA1 AI336848 0183 Early endosome antigen 1 316.227766 2.29 194.98446 212629_s_at PKN2 AI633689 0224 Protein kinase N2 67.60829754 2.06 114.8153621 216971_s_at PLEC1 Z54367 1015 “Plectin 1, intermediate 35.48133892 2.07 117.4897555 40 filament binding protein 500 kDa” 225289_at STAT3 AI139252 0174 Signal transducer and 416.8693835 2.82 660.693448 activator of transcription 3 (acute-phase response factor) 217713_x_at AA126763 0008 165.9586907 2.01 102.3292992 225361_x_at FAM122B AI348001 0187 Family with sequence 630.9573445 2.64 436.5158322 similarity 122B 242920_at AW590838 0520 331.1311215 2.1 125.8925412 41 227754_at AV700815 0447 “CDNA FLJ10417 fis, 173.7800829 1.93 85.11380382 42 clone NT2RP1000112” 226680_at BF056303 0614 Transcribed locus 213.796209 1.99 97.7237221 202157_s_at CUGBP2 U69546 0989 “CUG triplet repeat, RNA 1995.262315 3.14 1380.384265 binding protein 2” 208988_at BE675843 0589 190.5460718 2.11 128.8249552 222243_s_at TOB2 AB051450 0094 “Transducer of ERBB2, 2” 107.1519305 1.9 79.43282347 217862_at N24868 0746 Transcribed locus 194.98446 2.47 295.1209227 64486_at CORO1B AI341234 0185 “Coronin, actin binding 223.8721139 2.49 309.0295433 protein, 1B” 230918_at BE856598 0601 239.8832919 2.14 138.0384265 204978_at SFRS16 NM_007056 0873 “Splicing factor, 63.09573445 2.15 141.2537545 arginine/serine-rich 16” 232879_at CRTC3 AK024981 0354 CREB regulated 91.20108394 1.65 44.66835922 transcription coactivator 3 235032_at DNAJA5 BG112118 0672 DnaJ homology subfamily 251.1886432 2.13 134.8962883 A member 5 203591_s_at CSF3R NM_000760 0761 Colony stimulating factor 3 144.5439771 2.47 295.1209227 receptor (granulocyte) 228098_s_at MYLIP AW292746 0497 Myosin regulatory light 1047.128548 2.83 676.0829754 chain interacting protein 234734_s_at TNRC6A AK025696 0358 Trinucleotide repeat 181.9700859 2.48 301.995172 containing 6A 244433_at AI950023 0307 426.5795188 2.32 208.9296131 226641_at AU157224 0438 “CDNA FLJ11570 fis, 851.1380382 2.73 537.0317964 clone HEMBA1003309” 222791_at RSBN1 AK022166 0330 Round spermatid basic 1202.264435 2.75 562.3413252 protein 1 225706_at GLCCI1 AI761989 0259 Glucocorticoid induced 1000 2.73 537.0317964 transcript 1 243790_at ZNF585A AA203136 0015 Zinc finger protein 585A 154.8816619 1.85 70.79457844 244145_at BG260337 0683 251.1886432 2.19 154.8816619 203751_x_at JUND AI762296 0260 Jun D proto-oncogene 79.43282347 2.19 154.8816619 225216_at CXorf39 AI590719 0220 Chromosome X open 416.8693835 2.48 301.995172 reading frame 39 228853_at “(LOC730432, AI652546 0229 Serine/threonine/tyrosine 316.227766 2.33 213.796209 STYX)” interacting protein 232909_s_at “(BPTF, AU146870 0426 “(Bromodomain PHD 776.2471166 2.69 489.7788194 LOC646043)” finger transcription factor, Similar to Enhancer of bithorax CG32346-PB, isoform B)” 36564_at IBRDC3 W27419 0998 IBR domain containing 3 107.1519305 2.31 204.1737945 200073_s_at HNRPD M94630 0742 “Heterogeneous nuclear 1737.800829 3.08 1202.264435 ribonucleoprotein D (AU- rich element RNA binding protein 1, 37 kDa)” 200808_s_at ZYX NM_003461 0804 Zyxin 398.1071706 2.85 707.9457844 235125_x_at AI078279 0167 Transcribed locus 147.9108388 1.75 56.23413252 226712_at BF206389 0627 “CDNA: FLJ22100 fis, 199.5262315 2.48 301.995172 clone HEP17127” 208447_s_at PRPS1 NM_002764 0795 Phosphoribosyl 67.60829754 2.12 131.8256739 pyrophosphate synthetase 1 226426_at BG149849 0674 Transcribed locus 457.0881896 2.49 309.0295433 239163_at UBE2B AW364833 0507 Ubiquitin-conjugating 64.5654229 2.13 134.8962883 enzyme E2B (RAD6 homolog) 219426_at EIF2C3 NM_024852 0949 “Eukaryotic translation 43.65158322 1.86 72.44359601 initiation factor 2C, 3” 235341_at LOC144871 AL119957 0387 Hypothetical protein 199.5262315 2.55 354.8133892 LOC144871 242243_at TMF1 AI767435 0264 TATA element modulatory 102.3292992 1.66 45.70881896 factor 1 201236_s_at BTG2 NM_006763 0870 “BTG family, member 2” 281.8382931 2.63 426.5795188 202577_s_at DDX19A BC005162 0553 DEAD (Asp-Glu-Ala-As) 117.4897555 1.91 81.28305162 box polypeptide 19A 227772_at AV700849 0448 213.796209 2.09 123.0268771 229897_at ZNF641 BF195808 0626 Zinc finger protein 641 141.2537545 2.42 263.0267992 218566_s_at CHORDC1 NM_012124 0876 Cysteine and histidine-rich 213.796209 2.12 131.8256739 domain (CHORD)- containing 1 203839_s_at TNK2 NM_005781 0845 “Tyrosine kinase, non- 42.65795188 1.96 91.20108394 receptor, 2” 204361_s_at SKAP2 AB014486 0085 Src kinase associated 123.0268771 1.84 69.18309709 phosphoprotein 2 224250_s_at SECISBP2 BC001189 0541 SECIS binding protein 2 371.5352291 2.81 645.654229 225350_s_at ZYG11B AV701229 0449 Zyg-11 homolog B (C. elegans) 676.0829754 2.64 436.5158322 204516_at BG390306 0692 Transcribed locus 363.0780548 2.22 165.9586907 225620_at RAB35 AL534848 0412 “RAB35, member RAS 186.2087137 2.47 295.1209227 oncogene family” 226965_at FAM116A BF438017 0636 “(Family with sequence 812.8305162 2.72 524.8074602 similarity 116, member A, Transcribed locus)” 239808_at AI084489 0169 Transcribed locus 295.1209227 2.2 158.4893192 227428_at GABPA BE876628 0605 “GA binding protein 331.1311215 2.33 213.796209 transcription factor, alpha subunit 60 kDa” 218595_s_at “(HEATR1, NM_018072 0921 “Lectin, galactoside- 199.5262315 2.15 141.2537545 LGALS8)” binding, soluble, 8 (galectin 8)” 222266_at C19orf2 BF796940 0661 Chromosome 19 open 147.9108388 1.93 85.11380382 reading frame 2 239597_at AA993566 0080 114.8153621 2.43 269.1534804 203415_at PDCD6 NM_013232 0879 Programmed cell death 6 158.4893192 2.33 213.796209 208866_at BF510713 0642 CDNA clone 158.4893192 2 100 IMAGE: 4044084 212575_at C19orf6 BF966155 0665 Chromosome 19 open 2.398832919 1.47 29.51209227 reading frame 6 225176_at AA156754 0013 “CDNA FLJ42149 fis, 912.0108394 2.81 645.654229 clone THYMU1000692” 227223_at RBM39 BE466173 0575 RNA binding motif protein 165.9586907 2.58 380.1893963 39 41386_i_at JMJD3 AB002344 0082 Jumonji domain 223.8721139 2.58 380.1893963 containing 3 225995_x_at “(FAM39DP, BG178695 0675 “(CXYorf1-related protein, 281.8382931 2.67 467.7351413 FLJ00038, Family with sequence LOC376475, similarity 39, member D LOC727741)” pseudogene)” 228328_at KLHL28 AI982758 0311 Kelch-like 28 (Drosophila) 269.1534804 2.2 158.4893192 235409_at MGA AU149225 0429 MAX gene associated 77.62471166 2.27 186.2087137 200649_at NUCB1 BC002356 0544 Nucleobindin 1 158.4893192 2.46 288.4031503 232615_at AA632758 0034 Transcribed locus 1148.153621 2.75 562.3413252 205882_x_at ADD3 AI818488 0278 Adducin 3 (gamma) 1905.460718 3.11 1288.249552 228496_s_at CRIM1 AW243081 0489 Cysteine rich 151.3561248 1.85 70.79457844 transmembrane BMP regulator 1 (chordin-like) 209189_at FOS BC004490 0549 V-fos FBJ murine 407.3802778 3.14 1380.384265 osteosarcoma viral oncogene homolog 239233_at KIAA1212 AA744613 0053 KIAA1212 25.11886432 1.04 10.96478196 224308_s_at INTS2 AL136800 0393 Integrator complex subunit 2 95.4992586 1.68 47.86300923 208705_s_at EIF5 BG481972 0696 Eukaryotic translation 363.0780548 2.67 467.7351413 initiation factor 5 218607_s_at SDAD1 NM_018115 0922 SDA1 domain containing 1 173.7800829 2.42 263.0267992 200041_s_at BAT1 NM_004640 0826 HLA-B associated 870.96359 3.06 1148.153621 transcript 1 202850_at ABCD3 NM_002858 0796 “ATP-binding cassette, 199.5262315 2.11 128.8249552 sub-family D (ALD), member 3” 224562_at “(LOC644739, AK025566 0357 “(Similar to Wiskott- 870.96359 3.19 1548.816619 LOC647909, Aldrich syndrome protein WASF2)” family member 4 (WASP- family protein member 4), WAS protein family, member 2)” 222644_s_at GLT25D1 AI924150 0296 Glycosyltransferase 25 123.0268771 2.39 245.4708916 domain containing 1 212536_at ATP11B AB023173 0088 “ATPase, Class VI, type 147.9108388 1.99 97.7237221 11B” 215269_at TMEM1 AI922538 0294 Transmembrane protein 1 102.3292992 1.72 52.48074602 243303_at AA811657 0064 218.7761624 2.06 114.8153621 201991_s_at KIF5B BF223224 0630 Kinesin family member 5B 562.3413252 2.62 416.8693835 213327_s_at USP12 AI820101 0280 Ubiquitin specific 93.32543008 1.77 58.88436554 peptidase 12 213882_at TM2D1 AA012917 0001 TM2 domain containing 1 45.70881896 1.43 26.91534804 214715_x_at ZNF160 AK024789 0348 Zinc finger protein 160 234.4228815 2.15 141.2537545 225845_at ZBTB44 BG253884 0681 Zinc finger and BTB 645.654229 2.58 380.1893963 domain containing 44 215529_x_at DIP2A AI590053 0219 DIP2 disco-interacting 77.62471166 1.59 38.9045145 protein 2 homolog A (Drosophila) 242539_at LOC730069 AW665509 0523 Similar to nuclear receptor 213.796209 1.99 97.7237221 binding factor 2 203311_s_at ARF6 M57763 0735 ADP-ribosylation factor 6 169.8243652 2.51 323.5936569 205854_at TULP3 AK024246 0342 Tubby like protein 3 61.65950019 1.59 38.9045145 212042_x_at “(LOC653949, BG389744 0691 Ribosomal protein L7 3235.936569 3.37 2344.228815 RPL7, hCG_2015956, hCG_31916)” 233369_at AU146027 0424 “CDNA FLJ11835 fis, 263.0267992 2.17 147.9108388 clone HEMBA1006595” 212513_s_at USP33 AB029020 0089 Ubiquitin specific 331.1311215 2.4 251.1886432 peptidase 33 218626_at EIF4ENIF1 NM_019843 0930 Eukaryotic translation 125.8925412 1.98 95.4992586 initiation factor 4E nuclear import factor 1 208246_x_at NM_017618 0909 194.98446 2.08 120.2264435 224559_at MALAT1 AF001540 0104 Metastasis associated 309.0295433 3.15 1412.537545 lung adenocarcinoma transcript 1 (non-coding RNA) 205312_at SPI1 NM_003120 0798 Spleen focus forming virus 81.28305162 2.35 223.8721139 (SFFV) proviral integration oncogene spi1 213318_s_at BAT3 BG028844 0669 HLA-B associated 363.0780548 2.71 512.861384 transcript 3 212099_at RHOB AI263909 0179 “Ras homolog gene 208.9296131 2.7 501.1872336 family, member B” 223131_s_at TRIM8 AI925572 0299 Tripartite motif-containing 8 79.43282347 2.15 141.2537545 212487_at GPATCH8 AI673812 0234 G patch domain 37.15352291 1.94 87.096359 containing 8 200011_s_at ARF3 NM_001659 0775 ADP-ribosylation factor 3 891.2509381 3.1 1258.925412 210543_s_at “(LOC731751, U34994 0981 “Protein kinase, DNA- 162.1810097 2.07 117.4897555 PRKDC)” activated, catalytic polypeptide” 217313_at AC004692 0098 218.7761624 2.13 134.8962883 228106_at C4orf30 AA031528 0004 Chromosome 4 open 263.0267992 2.22 165.9586907 reading frame 30 218043_s_at AZI2 NM_022461 0940 5-azacytidine induced 2 77.62471166 1.57 37.15352291 203514_at MAP3K3 BF971923 0666 Mitogen-activated protein 162.1810097 2.02 104.7128548 kinase kinase kinase 3 223295_s_at LUC7L BE049621 0566 LUC7-like (S. cerevisiae) 467.7351413 2.47 295.1209227 235469_at MGC40405 AV744101 0457 Hypothetical protein 89.12509381 1.56 36.30780548 MGC40405 209440_at PRPS1 BC001605 0542 Phosphoribosyl 165.9586907 2.37 234.4228815 pyrophosphate synthetase 1 227039_at AKAP13 AI674926 0235 A kinase (PRKA) anchor 288.4031503 2.74 549.5408739 protein 13 218499_at RP6-213H19.1 NM_016542 0904 Serine/threonine protein 338.8441561 2.34 218.7761624 kinase MST4 232440_at ZDHHC13 AU155198 0433 “Zinc finger, DHHC-type 181.9700859 2.02 104.7128548 containing 13” 209727_at GM2A M76477 0737 GM2 ganglioside activator 10.23292992 1.77 58.88436554 241891_at T92908 0972 436.5158322 2.38 239.8832919 227525_at GLCCI1 AA058770 0006 Glucocorticoid induced 457.0881896 2.41 257.0395783 transcript 1 228088_at AI092265 0170 “CDNA FLJ31513 fis, 128.8249552 1.94 87.096359 clone NT2RI1000127” 242362_at AI797788 0269 489.7788194 2.33 213.796209 34478_at RAB11B X79780 1009 “RAB11B, member RAS 18.62087137 1.69 48.97788194 oncogene family” 223135_s_at BBX AL136769 0392 Bobby sox homolog 295.1209227 2.62 416.8693835 (Drosophila) 225780_at RSC1A1 AL565415 0418 “Regulatory solute carrier 316.227766 2.3 199.5262315 protein, family 1, member 1” 211791_s_at KCNAB2 AF044253 0112 “Potassium voltage-gated 20.41737945 1.98 95.4992586 channel, shaker-related subfamily, beta member 2” 204252_at CDK2 M68520 0736 Cyclin-dependent kinase 2 114.8153621 1.92 83.17637711 202420_s_at DHX9 NM_001357 0771 DEAH (Asp-Glu-Ala-His) 223.8721139 2.24 173.7800829 box polypeptide 9 223138_s_at DHX36 AI937206 0304 DEAH (Asp-Glu-Ala-His) 162.1810097 2.44 275.4228703 box polypeptide 36 240452_at GSPT1 AA580082 0030 G1 to S phase transition 1 316.227766 2.15 141.2537545 202082_s_at SEC14L1 AV748469 0458 SEC14-like 1 (S. cerevisiae) 54.95408739 1.98 95.4992586 213038_at IBRDC3 AL031602 0365 IBR domain containing 3 89.12509381 2.14 138.0384265 232038_at C6orf170 AI052103 0162 Chromosome 6 open 53.70317964 1.43 26.91534804 reading frame 170 229036_at TNRC6B AI681177 0238 “(Transcribed locus, 208.9296131 2.58 380.1893963 Trinucleotide repeat containing 6B)” 229235_at AI983432 0312 Transcribed locus 389.045145 2.41 257.0395783 226412_at C6orf111 N66397 0752 Chromosome 6 open 575.4399373 2.54 346.7368505 reading frame 111 212637_s_at WWP1 AU155187 0432 WW domain containing E3 41.68693835 1.4 25.11886432 ubiquitin protein ligase 1 220296_at NM_024564 0947 100 1.71 51.2861384 240695_at AA876138 0075 60.25595861 2.01 102.3292992 224759_s_at C12orf23 AK001731 0320 Chromosome 12 open 301.995172 2.26 181.9700859 reading frame 23 222794_x_at PAPD1 AK022188 0331 PAP associated domain 323.5936569 2.36 229.0867653 containing 1 224974_at SUDS3 AK024460 0344 Suppressor of defective 186.2087137 1.98 95.4992586 silencing 3 homolog (S. cerevisiae) 242650_at AW298590 0503 Transcribed locus 69.18309709 1.5 31.6227766 212921_at SMYD2 AF070592 0121 SET and MYND domain 75.8577575 1.64 43.65158322 containing 2 217717_s_at YWHAB BF246499 0631 “Tyrosine 3- 323.5936569 2.71 512.861384 monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide” 221419_s_at NM_013307 0880 107.1519305 2.35 223.8721139 204809_at CLPX NM_006660 0866 ClpX caseinolytic 97.7237221 1.85 70.79457844 peptidase X homolog (E. coli) 201409_s_at PPP1CB NM_002709 0794 “Protein phosphatase 1, 269.1534804 2.29 194.98446 catalytic subunit, beta isoform” 209829_at C6orf32 AB002384 0083 Chromosome 6 open 776.2471166 2.68 478.6300923 reading frame 32 225761_at PAPD4 AI434509 0203 PAP associated domain 602.5595861 2.63 426.5795188 containing 4 228471_at ANKRD44 AA744636 0054 Ankyrin repeat domain 44 562.3413252 2.51 323.5936569 201526_at ARF5 NM_001662 0776 ADP-ribosylation factor 5 162.1810097 2.39 245.4708916 241435_at AA702930 0044 1698.243652 2.9 794.3282347 227567_at AMZ2 AL524467 0407 Archaemetzincins-2 338.8441561 2.3 199.5262315 209563_x_at CALM1 BC000454 0537 “Calmodulin 1 691.8309709 3.07 1174.897555 (phosphorylase kinase, delta)” 242518_at AA748423 0056 74.13102413 2.07 117.4897555 239049_at BF514509 0644 239.8832919 2.12 131.8256739 209024_s_at SYNCRIP AI472757 0209 “Synaptotagmin binding, 138.0384265 2.31 204.1737945 cytoplasmic RNA interacting protein” 211948_x_at BAT2D1 BG261071 0685 BAT2 domain containing 1 102.3292992 2.45 281.8382931 228446_at KIAA2026 BF062203 0616 KIAA2026 338.8441561 2.38 239.8832919 229541_at BE669703 0583 “CDNA FLJ38918 fis, 93.32543008 2.27 186.2087137 clone NT2NE2010633” 237330_at AA603494 0033 Transcribed locus 91.20108394 1.56 36.30780548 217842_at LUC7L2 NM_016019 0893 LUC7-like 2 (S. cerevisiae) 61.65950019 1.61 40.73802778 201828_x_at FAM127A NM_003928 0809 “Family with sequence 213.796209 2.43 269.1534804 similarity 127, member A” 229366_at BG149765 0673 Transcribed locus 218.7761624 2.22 165.9586907 201986_at THRAP1 AB011165 0084 Thyroid hormone receptor 323.5936569 2.35 223.8721139 associated protein 1 202373_s_at RAB3GAP2 AF255648 0148 RAB3 GTPase activating 288.4031503 2.33 213.796209 protein subunit 2 (non- catalytic) 241906_at BF001773 0612 281.8382931 2.13 134.8962883 201318_s_at “(MRCL3, NM_006471 0863 “(Myosin regulatory light 1778.27941 3.13 1348.962883 MRLC2)” chain MRCL3, Myosin regulatory light chain MRLC2)” 207941_s_at RBM39 NM_004902 0830 RNA binding motif protein 707.9457844 2.72 524.8074602 39 229586_at CHD9 AW300405 0505 Chromodomain helicase 102.3292992 2.23 169.8243652 DNA binding protein 9 217336_at AL118510 0385 190.5460718 2.06 114.8153621 209648_x_at SOCS5 AL136896 0394 Suppressor of cytokine 38.9045145 1.32 20.89296131 signaling 5 226664_at TBC1D20 AL121747 0388 “TBC1 domain family, 199.5262315 2.44 275.4228703 member 20” 225786_at LOC284702 AI440495 0204 Hypothetical protein 281.8382931 2.25 177.827941 LOC284702 208635_x_at NACA BF976260 0667 Nascent-polypeptide- 5128.61384 3.62 4168.693835 associated complex alpha polypeptide 223444_at SENP7 AL136599 0391 SUMO1/sentrin specific 229.0867653 2.09 123.0268771 peptidase 7 208975_s_at KPNB1 L38951 0725 Karyopherin (importin) 147.9108388 1.98 95.4992586 beta 1 208935_s_at LGALS8 L78132 0727 “Lectin, galactoside- 151.3561248 1.96 91.20108394 binding, soluble, 8 (galectin 8)” 200847_s_at TMEM66 NM_016127 0895 Transmembrane protein 1258.925412 2.99 977.237221 66 218247_s_at RKHD2 NM_016626 0906 Ring finger and KH 208.9296131 2.04 109.6478196 domain containing 2 227121_at BF476076 0640 MRNA; cDNA 407.3802778 2.43 269.1534804 DKFZp586K1922 (from clone DKFZp586K1922) 235984_at AL036662 0367 Transcribed locus 100 2.27 186.2087137 212069_s_at KIAA0515 AK026025 0360 KIAA0515 77.62471166 2.13 134.8962883 243649_at AI678692 0236 141.2537545 1.88 75.8577575 238549_at AI420611 0201 Transcribed locus 316.227766 2.35 223.8721139 233093_s_at BIRC6 AK023788 0339 Baculoviral IAP repeat- 851.1380382 2.83 676.0829754 containing 6 (apollon) 221749_at YTHDF3 AU157915 0439 “YTH domain family, 234.4228815 2.16 144.5439771 member 3” 242726_at BF221850 0629 Transcribed locus 128.8249552 1.81 64.5654229 242195_x_at NUMBL BE350811 0573 Numb homolog 588.8436554 2.6 398.1071706 (Drosophila)-like 204020_at PURA BF739943 0658 Purine-rich element 316.227766 2.36 229.0867653 binding protein A 208694_at PRKDC U47077 0984 “Protein kinase, DNA- 131.8256739 1.94 87.096359 activated, catalytic polypeptide” 200047_s_at YY1 NM_003403 0802 YY1 transcription factor 676.0829754 2.72 524.8074602 228097_at MYLIP AW292746 0497 Myosin regulatory light 354.8133892 2.35 223.8721139 chain interacting protein 213605_s_at AL049987 0376 MRNA; cDNA 144.5439771 1.76 57.54399373 DKFZp564F112 (from clone DKFZp564F112) 218259_at MKL2 NM_014048 0881 MKL/myocardin-like 2 104.7128548 1.83 67.60829754 240338_at LRAP AI807341 0272 Leukocyte-derived 57.54399373 1.45 28.18382931 arginine aminopeptidase 226366_at SHPRH AI828221 0285 SNF2 histone linker PHD 173.7800829 2.12 131.8256739 RING helicase 218237_s_at SLC38A1 NM_030674 0955 “Solute carrier family 38, 851.1380382 2.65 446.6835922 member 1” 201473_at JUNB NM_002229 0783 Jun B proto-oncogene 346.7368505 2.83 676.0829754 226786_at RFX1 BF507952 0641 “Regulatory factor X, 1 363.0780548 2.72 524.8074602 (influences HLA class II expression)” 214948_s_at AL050136 0377 MRNA; cDNA 181.9700859 2.11 128.8249552 DKFZp586L141 (from clone DKFZp586L141) 225672_at GOLGA2 AL514295 0405 “Golgi autoantigen, golgin 338.8441561 2.65 446.6835922 subfamily a, 2” 229787_s_at OGT AI742039 0251 O-linked N- 257.0395783 2.08 120.2264435 acetylglucosamine (GlcNAc) transferase (UDP-N- acetylglucosamine:polypeptide- N- acetylglucosaminyl transferase) 202253_s_at DNM2 NM_004945 0832 Dynamin 2 85.11380382 2.15 141.2537545 225564_at SPATA13 AW269397 0493 Spermatogenesis 933.2543008 2.74 549.5408739 associated 13 218967_s_at PTER NM_030664 0954 Phosphotriesterase 128.8249552 1.93 85.11380382 related 217007_s_at ADAM15 AK000667 0316 ADAM metallopeptidase 7.58577575 1.54 34.67368505 domain 15 (metargidin) 228250_at FNIP1 AW263086 0491 Folliculin interacting 60.25595861 2.16 144.5439771 protein 1 212291_at HIPK1 AI393355 0199 Homeodomain interacting 117.4897555 2.36 229.0867653 protein kinase 1 203203_s_at KRR1 NM_007043 0872 “KRR1, small subunit 85.11380382 1.71 51.2861384 (SSU) processome component, homolog (yeast)” 229470_at FAM105B AW451634 0509 “Family with sequence 257.0395783 2.22 165.9586907 similarity 105, member B” 224698_at FAM62B AB033054 0090 Family with sequence 676.0829754 2.63 426.5795188 similarity 62 (C2 domain containing) member B 244061_at AI510829 0213 275.4228703 2.07 117.4897555 204075_s_at KIAA0562 NM_014704 0887 KIAA0562 24.54708916 1.07 11.74897555 217019_at AL137162 0395 66.0693448 1.45 28.18382931 218600_at LIMD2 NM_030576 0953 LIM domain containing 2 102.3292992 2.28 190.5460718 213606_s_at ARHGDIA AI571798 0218 Rho GDP dissociation 25.70395783 1.88 75.8577575 inhibitor (GDI) alpha 201260_s_at SYPL1 NM_006754 0869 Synaptophysin-like 1 301.995172 2.3 199.5262315 234340_at AK021431 0324 “CDNA FLJ11369 fis, 50.11872336 1.45 28.18382931 clone HEMBA1000338” 207686_s_at CASP8 NM_001228 0770 “Caspase 8, apoptosis- 61.65950019 2.13 134.8962883 related cysteine peptidase” 201332_s_at STAT6 NM_003153 0799 “Signal transducer and 102.3292992 2.18 151.3561248 activator of transcription 6, interleukin-4 induced” 203388_at ARRB2 NM_004313 0819 “Arrestin, beta 2” 457.0881896 2.85 707.9457844 204275_at SOLH AI796687 0268 Small optic lobes homolog 52.48074602 1.9 79.43282347 (Drosophila) 238057_at USP45 AW195800 0487 Ubiquitin specific 81.28305162 1.55 35.48133892 peptidase 45 242352_at NIPBL AW272262 0494 Nipped-B homolog 60.25595861 2.21 162.1810097 (Drosophila) 212846_at RRP1B AA811192 0063 KIAA0179 323.5936569 2.41 257.0395783 212090_at GRINA AL571424 0420 “Glutamate receptor, 97.7237221 2.27 186.2087137 ionotropic, N-methyl D- asparate-associated protein 1 (glutamate binding)” 227636_at THAP5 BG500677 0698 THAP domain containing 5 194.98446 2.05 112.2018454 209379_s_at KIAA1128 AF241785 0147 KIAA1128 213.796209 2.16 144.5439771 230180_at AA521056 0025 91.20108394 2.37 234.4228815 217489_s_at IL6R S72848 0968 Interleukin 6 receptor 27.54228703 1.77 58.88436554 200014_s_at “(HNRPC, NM_004500 0824 Heterogeneous nuclear 512.861384 2.63 426.5795188 hCG_1641229)” ribonucleoprotein C (C1/C2) 221628_s_at N-PAC AF326966 0155 Cytokine-like nuclear 42.65795188 1.95 89.12509381 factor n-pac 214594_x_at ATP8B1 BG252666 0680 “ATPase, Class I, type 8B, 147.9108388 1.79 61.65950019 member 1” 218528_s_at RNF38 NM_022781 0941 Ring finger protein 38 309.0295433 2.38 239.8832919 223494_at MGEA5 AF307332 0152 Meningioma expressed 1659.586907 3.05 1122.018454 antigen 5 (hyaluronidase) 234260_at AL122039 0390 MRNA; cDNA 97.7237221 1.68 47.86300923 DKFZp434E0572 (from clone DKFZp434E0572) 203104_at CSF1R NM_005211 0838 “Colony stimulating factor 354.8133892 2.84 691.8309709 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog” 221755_at EHBP1L1 BG334196 0688 EH domain binding protein 47.86300923 1.95 89.12509381 1-like 1 200976_s_at TAX1BP1 NM_006024 0850 Tax1 (human T-cell 691.8309709 2.74 549.5408739 leukemia virus type I) binding protein 1 212297_at ATP13A3 BF218804 0628 ATPase type 13A3 100 1.77 58.88436554 208841_s_at G3BP2 AB014560 0086 GTPase activating protein 354.8133892 2.41 257.0395783 (SH3 domain) binding protein 2 200632_s_at NDRG1 NM_006096 0853 N-myc downstream 223.8721139 2.49 309.0295433 regulated gene 1 215383_x_at SPG21 AL137312 0397 “Spastic paraplegia 21, 194.98446 2.08 120.2264435 maspardin (autosomal recessive, Mast syndrome)” 235493_at AI927329 0300 Transcribed locus 213.796209 2.05 112.2018454 236614_at LOC729683 AW006288 0463 Hypothetical protein 177.827941 2.38 239.8832919 LOC729683 209273_s_at ISCA1 BG387555 0690 Iron-sulfur cluster 144.5439771 2 100 assembly 1 homolog (S. cerevisiae) 227621_at WTAP BE464729 0574 Wilms tumor 1 associated 1584.893192 3.07 1174.897555 protein 225431_x_at ACY1L2 BE779764 0596 Aminoacylase 1-like 2 269.1534804 2.09 123.0268771 235879_at AI697540 0245 Transcribed locus 870.96359 2.61 407.3802778 226825_s_at TMEM165 AW665624 0524 Transmembrane protein 575.4399373 2.98 954.992586 165 218143_s_at SCAMP2 NM_005697 0843 Secretory carrier 239.8832919 2.54 346.7368505 membrane protein 2 203890_s_at DAPK3 BF686824 0655 Death-associated protein 25.70395783 1.64 43.65158322 kinase 3 208313_s_at SF1 NM_004630 0825 Splicing factor 1 467.7351413 2.82 660.693448 211352_s_at NCOA3 U80737 0991 Nuclear receptor 54.95408739 2.02 104.7128548 coactivator 3 224579_at SLC38A1 BF247552 0632 “Solute carrier family 38, 1380.384265 2.98 954.992586 member 1” 201752_s_at ADD3 AI763123 0262 Adducin 3 (gamma) 1819.700859 3.1 1258.925412 231747_at CYSLTR1 NM_006639 0864 Cysteinyl leukotriene 371.5352291 2.81 645.654229 receptor 1 208319_s_at RBM3 NM_006743 0868 “RNA binding motif 407.3802778 2.39 245.4708916 (RNP1, RRM) protein 3” 227159_at GHDC AI827015 0284 GH3 domain containing 199.5262315 2.47 295.1209227 230387_at AL038450 0371 Transcribed locus 218.7761624 2.1 125.8925412

TABLE 3 Fragment Id Name SEQ ID NO. Accession Symbol Gene Name 235101 204439_at 0871 NM_006820 IFI44L interferon-induced protein 44-like 273089 242625_at 0483 AW189843 RSAD2 radical S-adenosyl methionine domain containing 2 244312 213797_at 0184 AI337069 RSAD2 radical S-adenosyl methionine domain containing 2 244967 214453_s_at 0860 NM_006417 IFI44 interferon-induced protein 44 272333 241869_at 0469 AW026509 APOL6 apolipoprotein L, 6 232750 202086_at 0786 NM_002462 MX1 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) 243517 212999_x_at 0496 AW276186 LOC650557 similar to HLA class II histocompatibility antigen, DQ(W1.1) beta chain precursor (DQB1*0501) 259919 229450_at 0166 AI075407 IFIT3 interferon-induced protein with tetratricopeptide repeats 3 232809 202145_at 0785 NM_002346 LY6E lymphocyte antigen 6 complex, locus E 236145 205483_s_at 0835 NM_005101 ISG15 ISG15 ubiquitin-like modifier 262204 231735_s_at 0882 NM_014086 243866 213350_at 0654 BF680255 RPS11 ribosomal protein S11 261953 231484_at 0202 AI424825 245632 215123_at 0375 AL049250 236794 206133_at 0908 NM_017523 XAF1 XIAP associated factor-1 257172 226702_at 0252 AI742057 LOC129607 hypothetical protein LOC129607 244573 214059_at 0565 BE049439 IFI44 interferon-induced protein 44 241463 210873_x_at 0973 U03891 APOBEC3A apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A 250106 219607_s_at 0945 NM_024021 MS4A4A membrane-spanning 4-domains, subfamily A, member 4 257227 226757_at 0009 AA131041 IFIT2 interferon-induced protein with tetratricopeptide repeats 2 269075 238611_at 0292 AI906424 235409 204747_at 0772 NM_001549 IFIT3 interferon-induced protein with tetratricopeptide repeats 3 268477 238013_at 0634 BF347859 265621 235157_at 0501 AW297731 247363 216858_x_at 0379 AL080112 235077 204415_at 0942 NM_022873 IFI6 interferon, alpha-inducible protein 6 235634 204972_at 0907 NM_016817 OAS2 2′-5′-oligoadenylate synthetase 2, 69/71 kDa 263006 232537_x_at 0440 AU159474 MARK3 MAP/microtubule affinity-regulating kinase 3 272288 241824_at 0002 AA019641 264429 233964_at 0381 AL110135 268332 237868_x_at 0267 AI791828 247318 216813_at 0402 AL512728 245901 215392_at 0428 AU148154 272081 241617_x_at 0607 BE961949 245771 215262_at 0115 AF052160 118805 44673_at 0748 N53555 SIGLEC1 sialic acid binding Ig-like lectin 1, sialoadhesin 249851 219352_at 0915 NM_017912 HERC6 hect domain and RLD 6 245223 214712_at 0340 AK023827 RUNDC2B RUN domain containing 2B 238391 207735_at 0913 NM_017831 RNF125 ring finger protein 125 236214 205552_s_at 0787 NM_002534 OAS1 2′,5′-oligoadenylate synthetase 1, 40/46 kDa 267022 236558_at 0043 AA699809 255042 224568_x_at 0462 AW005982 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non- coding RNA) 273157 242693_at 0522 AW664859 233351 202687_s_at 0987 U57059 TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 259086 228617_at 0011 AA142842 XAF1 XIAP associated factor-1 254068 223577_x_at 0068 AA827878 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non- coding RNA) 268806 238342_at 0653 BF677084 273735 243271_at 0164 AI064690 258078 227609_at 0035 AA633203 EPSTI1 epithelial stromal interaction 1 (breast) 274457 243993_at 0020 AA436887 250190 219691_at 0911 NM_017654 SAMD9 sterile alpha motif domain containing 9 231959 201295_s_at 0620 BF111821 WSB1 WD repeat and SOCS box-containing 1 235195 204533_at 0774 NM_001565 CXCL10 chemokine (C—X—C motif) ligand 10 247438 216933_x_at 0967 S67788 APC adenomatosis polyposis coli 244919 214405_at 1014 Z39557 249708 219209_at 0938 NM_022168 IFIH1 interferon induced with helicase C domain 1 258895 228426_at 0492 AW268886 CLEC2D C-type lectin domain family 2, member D 255711 225239_at 0188 AI355441 241858 211300_s_at 0718 K03199 TP53 tumor protein p53 (Li-Fraumeni syndrome) 248900 218400_at 0854 NM_006187 OAS3 2′-5′-oligoadenylate synthetase 3, 100 kDa 260469 230000_at 0214 AI523817 RNF213 ring finger protein 213 254430 223940_x_at 0134 AF132202 250362 219863_at 0899 NM_016323 HERC5 hect domain and RLD 5 274878 244414_at 0175 AI148006 267794 237330_at 0033 AA603494 274252 243788_at 0060 AA789293 246704 216197_at 0328 AK021569 ATF7IP activating transcription factor 7 interacting protein 263872 233406_at 0329 AK022100 241392 210797_s_at 0117 AF063612 OASL 2′-5′-oligoadenylate synthetase-like 239530 208900_s_at 0468 AW025108 TOP1 topoisomerase (DNA) I 266011 235547_at 0701 BG548427 270025 239561_at 0059 AA780679 263432 232964_at 0396 AL137266 LOC441257 hypothetical LOC441257 LOC442609 similar to Williams Beuren syndrome chromosome region 19 WBSCR19 Williams Beuren syndrome chromosome region 19 252807 222313_at 0528 AW972359 258499 228030_at 0161 AI041522 RBM6 RNA binding motif protein 6 252260 221765_at 0196 AI378044 UGCG UDP-glucose ceramide glucosyltransferase 254110 223619_x_at 0133 AF119841 PECR peroxisomal trans-2-enoyl-CoA reductase 265453 234989_at 0445 AV699657 TncRNA trophoblast-derived noncoding RNA 252824 222330_at 0530 AW974995 242071 211530_x_at 0740 M90686 HLA-G HLA-G histocompatibility antigen, class I, G 241567 210985_s_at 0116 AF056322 SP100 SP100 nuclear antigen 246107 215599_at 1012 X83300 GUSBP1 glucuronidase, beta pseudogene 1 LOC730390 similar to SMA4 SMA4 SMA4 275143 244679_at 0160 AI032730 244135 213620_s_at 0007 AA126728 ICAM2 intercellular adhesion molecule 2 274272 243808_at 0486 AW193531 234059 203397_s_at 0618 BF063271 GALNT3 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- acetylgalactosaminyltransferase 3 (GalNAc-T3) 272396 241932_at 0165 AI073803 251201 220702_at 0925 NM_018616 246681 216174_at 0356 AK025343 HCRP1 hepatocellular carcinoma-related HCRP1 247070 216565_x_at 0389 AL121994 239595 208965_s_at 0682 BG256677 IFI16 interferon, gamma-inducible protein 16 246029 215521_at 0335 AK023029 PHC3 polyhomeotic homolog 3 (Drosophila) 272488 242024_at 0971 T90999 274112 243648_at 0017 AA280627 ZC3H11A zinc finger CCCH-type containing 11A 264725 234260_at 0390 AL122039 271008 240544_at 0745 N23033 261578 231109_at 0962 R44974 244828 214314_s_at 0567 BE138647 EIF5B eukaryotic translation initiation factor 5B 238481 207827_x_at 0724 L36675 SNCA synuclein, alpha (non A4 component of amyloid precursor) 235128 204466_s_at 0684 BG260394 SNCA synuclein, alpha (non A4 component of amyloid precursor) 265641 235177_at 0221 AI625022 FAM119A family with sequence similarity 119, member A 233540 202876_s_at 0789 NM_002586 PBX2 pre-B-cell leukemia homeobox 2 263328 232860_x_at 0337 AK023732 RBM41 RNA binding motif protein 41 242745 212224_at 0759 NM_000689 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 252300 221805_at 0413 AL537457 NEFL neurofilament, light polypeptide 68 kDa 256137 225665_at 0173 AI129320 ZAK sterile alpha motif and leucine zipper containing kinase AZK 252427 221932_s_at 0010 AA133341 GLRX5 glutaredoxin 5 homolog (S. cerevisiae) 258398 227929_at 0431 AU151342 257281 226811_at 0372 AL046017 FAM46C family with sequence similarity 46, member C 239330 208700_s_at 0720 L12711 TKT transketolase (Wernicke-Korsakoff syndrome) 257126 226656_at 0467 AW024741 CRTAP cartilage associated protein

TABLE 4 Fragment Id Name SEQ ID NO. Accession Symbol Gene Name 255042 224568_x_at 0462 AW005982 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) 254430 223940_x_at 0134 AF132202 269238 238774_at 0526 AW960454 272333 241869_at 0469 AW026509 APOL6 apolipoprotein L, 6 255041 224567_x_at 0699 BG534952 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) 257145 226675_s_at 1002 W80468 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) 238469 207815_at 0792 NM_002620 PF4V1 platelet factor 4 variant 1 247363 216858_x_at 0379 AL080112 272488 242024_at 0971 T90999 245632 215123_at 0375 AL049250 238391 207735_at 0913 NM_017831 RNF125 ring finger protein 125 239530 208900_s_at 0468 AW025108 TOP1 topoisomerase (DNA) I 265492 235028_at 0686 BG288330 235672 205010_at 0929 NM_019067 GNL3L guanine nucleotide binding protein-like 3 (nucleolar)-like 268477 238013_at 0634 BF347859 240326 209703_x_at 0550 BC004492 METTL7A methyltransferase like 7A 247318 216813_at 0402 AL512728 255711 225239_at 0188 AI355441 262881 232412_at 0347 AK024690 273238 242774_at 0242 AI684761 SYNE2 spectrin repeat containing, nuclear envelope 2 257532 227062_at 0434 AU155361 TncRNA trophoblast-derived noncoding RNA 247055 216550_x_at 1010 X80821 ANKRD12 ankyrin repeat domain 12 241039 210426_x_at 0974 U04897 RORA RAR-related orphan receptor A 263432 232964_at 0396 AL137266 LOC441257 hypothetical LOC441257 LOC442609 similar to Williams Beuren syndrome chromosome region 19 WBSCR19 Williams Beuren syndrome chromosome region 19 265852 235388_at 0700 BG538482 CHD9 chromodomain helicase DNA binding protein 9 268332 237868_x_at 0267 AI791828 264429 233964_at 0381 AL110135 137612 60815_at 0031 AA601208 LOC441257 hypothetical LOC441257 249611 219112_at 0900 NM_016340 RAPGEF6 Rap guanine nucleotide exchange factor (GEF) 6 272343 241879_at 0513 AW511222 245894 215385_at 0334 AK022473 251439 220940_at 0952 NM_025190 KIAA1641 KIAA1641 248290 217790_s_at 0874 NM_007107 SSR3 signal sequence receptor, gamma (translocon-associated protein gamma) 232068 201404_x_at 0536 BC000268 PSMB2 proteasome (prosome, macropain) subunit, beta type, 2 246382 215874_at 0361 AK026820 247438 216933_x_at 0967 S67788 APC adenomatosis polyposis coli 246107 215599_at 1012 X83300 GUSBP1 glucuronidase, beta pseudogene 1 LOC730390 similar to SMA4 SMA4 SMA4 270035 239571_at 0172 AI123399 260649 230180_at 0025 AA521056 273380 242916_at 0037 AA642477 CEP110 centrosomal protein 110 kDa 272196 241732_at 0643 BF513820 274821 244357_at 0970 T90760 244165 213650_at 0464 AW006438 GOLGA8A golgi autoantigen, golgin subfamily a, 8A 245771 215262_at 0115 AF052160 252807 222313_at 0528 AW972359 274112 243648_at 0017 AA280627 ZC3H11A zinc finger CCCH-type containing 11A 248204 217704_x_at 0281 AI820796 SUZ12P suppressor of zeste 12 homolog pseudogene 241090 210479_s_at 0722 L14611 RORA RAR-related orphan receptor A 245901 215392_at 0428 AU148154 241969 211424_x_at 0130 AF113007 METTL7A methyltransferase like 7A 251085 220586_at 0951 NM_025134 CHD9 chromodomain helicase DNA binding protein 9 257461 226991_at 0023 AA489681 NFATC2 nuclear factor of activated T-cells, cytoplasmic, calcineurin- dependent 2 268805 238341_at 0653 BF677084 255023 224549_x_at 0142 AF194537 243107 212587_s_at 0273 AI809341 PTPRC protein tyrosine phosphatase, receptor type, C 270156 239692_at 0168 AI083578 262855 232386_at 0450 AV703288 VPS13C vacuolar protein sorting 13 homolog C (S. cerevisiae) 262458 231989_s_at 0095 AC003007 SMG1 PI-3-kinase-related kinase SMG-1 252481 221986_s_at 0465 AW006750 KLHL24 kelch-like 24 (Drosophila) 238601 207953_at 0106 AF010144 AD7C-NTP neuronal thread protein AD7c-NTP 269722 239258_at 0578 BE551407 274495 244031_at 0072 AA868193 273155 242691_at 0070 AA829017 241975 211430_s_at 0739 M87789 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 265453 234989_at 0445 AV699657 TncRNA trophoblast-derived noncoding RNA 269566 239102_s_at 0500 AW293296 236769 206108_s_at 0856 NM_006275 SFRS6 splicing factor, arginine/serine-rich 6 274342 243878_at 0177 AI248610 242548 212027_at 0298 AI925305 RBM25 RNA binding motif protein 25 274316 243852_at 0308 AI963460 252824 222330_at 0530 AW974995 271008 240544_at 0745 N23033 272689 242225_at 0216 AI569482 245204 214693_x_at 0593 BE732345 LOC727908 hypothetical protein LOC727908 LOC728936 similar to CG10522-PA LOC728980 hypothetical protein LOC728980 NBPF1 neuroblastoma breakpoint family, member 1 NBPF11 neuroblastoma breakpoint family, member 11 NBPF14 neuroblastoma breakpoint family, member 14 NBPF15 neuroblastoma breakpoint family, member 15 259656 229187_at 0159 AI026708 LOC283788 hypothetical protein LOC283788 246029 215521_at 0335 AK023029 PHC3 polyhomeotic homolog 3 (Drosophila) 272833 242369_x_at 0215 AI561070 239243 208610_s_at 0233 AI655799 SRRM2 serine/arginine repetitive matrix 2 243962 213446_s_at 0237 AI679073 IQGAP1 IQ motif containing GTPase activating protein 1 264616 234151_at 0346 AK024629 231152 AFFX-r2- 0729 M10098 Hs18SrRNA- M_x_at 261953 231484_at 0202 AI424825 274272 243808_at 0486 AW193531 264020 233554_at 0157 AF339764 245521 215012_at 0423 AU144775 247997 217497_at 0521 AW613387 273343 242879_x_at 0305 AI939442 265524 235060_at 0373 AL047052 DKFZp547E087 hypothetical gene LOC283846 251975 221477_s_at 0647 BF575213 SOD2 superoxide dismutase 2, mitochondrial 248110 217610_at 0374 AL047879 244919 214405_at 1014 Z39557 252260 221765_at 0196 AI378044 UGCG UDP-glucose ceramide glucosyltransferase 245538 215029_at 0383 AL117451 268267 237803_x_at 0021 AA455236 265068 234604_at 0350 AK024881 239886 209257_s_at 0660 BF795297 SMC3 structural maintenance of chromosomes 3 239489 208859_s_at 0227 AI650257 ATRX alpha thalassemia/mental retardation syndrome X-linked (RAD54 LOC728849 homolog, S. cerevisiae) similar to transcriptional regulator ATRX isoform 1 236256 205594_at 0890 NM_014897 ZNF652 zinc finger protein 652 242515 211993_at 0266 AI768512 WNK1 WNK lysine deficient protein kinase 1 268806 238342_at 0653 BF677084 254110 223619_x_at 0133 AF119841 PECR peroxisomal trans-2-enoyl-CoA reductase 261578 231109_at 0962 R44974 263939 233473_x_at 0437 AU156202 266109 235645_at 0512 AW501507 ESCO1 establishment of cohesion 1 homolog 1 (S. cerevisiae) 266011 235547_at 0701 BG548427 246096 215588_x_at 0352 AK024958 RIOK3 RIO kinase 3 (yeast) 270605 240141_at 0617 BF062399 270275 239811_at 0664 BF954306 242529 212007_at 0301 AI927512 UBXD2 UBX domain containing 2 264725 234260_at 0390 AL122039 237626 206965_at 0898 NM_016285 KLF12 Kruppel-like factor 12 233810 203147_s_at 0608 BE962483 TRIM14 tripartite motif-containing 14 274340 243876_at 0062 AA806845 246372 215864_at 0355 AK025077 262735 232266_x_at 0343 AK024379 CDC2L5 cell division cycle 2-like 5 (cholinesterase-related cell division controller) 267016 236552_at 0261 AI762475 265187 234723_x_at 0350 AK024881 239295 208663_s_at 0230 AI652848 TTC3 tetratricopeptide repeat domain 3 269628 239164_at 0586 BE674896 244440 213926_s_at 0254 AI742626 HRB HIV-1 Rev binding protein 274283 243819_at 0425 AU146329 264641 234176_at 0349 AK024877 259455 228986_at 0531 AW978375 OSBPL8 oxysterol binding protein-like 8 239465 208835_s_at 0478 AW089673 CROP cisplatin resistance-associated overexpressed protein 247068 216563_at 1010 X80821 ANKRD12 ankyrin repeat domain 12 246736 216229_x_at 1011 X81001 HCG2P7 HLA complex group 2 pseudogene 7 267786 237322_at 0293 AI914323 MIAT myocardial infarction associated transcript (non-protein coding) 231366 200702_s_at 0693 BG421209 DDX24 DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 262879 232410_at 0694 BG428861 243866 213350_at 0654 BF680255 RPS11 ribosomal protein S11 272288 241824_at 0002 AA019641 241872 211317_s_at 0111 AF041461 CFLAR CASP8 and FADD-like apoptosis regulator 253530 223036_at 0708 D84430 FARSB phenylalanyl-tRNA synthetase, beta subunit 240136 209508_x_at 0105 AF005774 CFLAR CASP8 and FADD-like apoptosis regulator 251203 220704_at 0924 NM_018563 267085 236621_at 0444 AV683684 242600 212079_s_at 0046 AA715041 MLL myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 238023 207365_x_at 0888 NM_014709 USP34 ubiquitin specific peptidase 34 238386 207730_x_at 0916 NM_017932 243314 212794_s_at 0319 AK001728 KIAA1033 KIAA1033 266926 236462_at 0051 AA742310 265631 235167_at 0611 BE972419 266723 236259_at 0635 BF433725 STK4 serine/threonine kinase 4 240866 210251_s_at 0129 AF112221 RUFY3 RUN and FYVE domain containing 3 245168 214657_s_at 0421 AU134977 TncRNA trophoblast-derived noncoding RNA 269022 238558_at 0205 AI445833 273291 242827_x_at 0061 AA806368 264284 233819_s_at 0336 AK023499 ZNF294 zinc finger protein 294 246694 216187_x_at 0146 AF222691 236717 206056_x_at 1007 X52075 SPN sialophorin (leukosialin, CD43) 52 AFFX- 0729 M10098 HUMRGE/ M10098_3_at 243544 213026_at 0609 BE965998 ATG12 ATG12 autophagy related 12 homolog (S. cerevisiae) 269715 239251_at 0527 AW963634 246037 215529_x_at 0219 AI590053 DIP2A DIP2 disco-interacting protein 2 homolog A (Drosophila) 239887 209258_s_at 0193 AI373676 SMC3 structural maintenance of chromosomes 3 250837 220338_at 0920 NM_018037 RALGPS2 Ral GEF with PH domain and SH3 binding motif 2 244471 213957_s_at 0036 AA635523 CEP350 centrosomal protein 350 kDa 234292 203630_s_at 0859 NM_006348 COG5 component of oligomeric golgi complex 5 252480 221985_at 0465 AW006750 KLHL24 kelch-like 24 (Drosophila) 237212 206551_x_at 0910 NM_017644 KLHL24 kelch-like 24 (Drosophila) 247346 216841_s_at 1006 X15132 SOD2 superoxide dismutase 2, mitochondrial 232118 201454_s_at 0471 AW055008 NPEPPS aminopeptidase puromycin sensitive 246112 215604_x_at 0338 AK023783 268974 238510_at 0055 AA744964 ZNF720 zinc finger protein 720 250731 220232_at 0950 NM_024906 SCD5 stearoyl-CoA desaturase 5 262594 232125_at 0427 AU147419 233043 202379_s_at 0190 AI361805 NKTR natural killer-tumor recognition sequence 269738 239274_at 0454 AV729557 238885 208246_x_at 0909 NM_017618 271687 241223_x_at 0282 AI821721 231749 201085_s_at 0040 AA664291 SON SON DNA binding protein 245712 215203_at 0508 AW438464 105867 39313_at 0081 AB002342 WNK1 WNK lysine deficient protein kinase 1 241338 210742_at 0118 AF064103 CDC14A CDC14 cell division cycle 14 homolog A (S. cerevisiae) 248079 217579_x_at 0506 AW301806 258784 228315_at 0223 AI632728 262204 231735_s_at 0882 NM_014086 267022 236558_at 0043 AA699809 270061 239597_at 0080 AA993566 273495 243031_at 0753 N90377 266718 236254_at 0564 BE048857 VPS13B vacuolar protein sorting 13 homolog B (yeast) 264495 234030_at 0125 AF090925 274975 244511_at 0446 AV700591 239717 209088_s_at 0969 T70262 UBN1 ubinuclein 1 236173 205511_at 0918 NM_017976 260682 230213_at 0569 BE220399 C19orf43 chromosome 19 open reading frame 43 253127 222633_at 0149 AF268193 TBL1XR1 transducin (beta)-like 1X-linked receptor 1 242364 211833_s_at 0977 U19599 BAX BCL2-associated X protein 264377 233912_x_at 0327 AK021525 261710 231241_at 0511 AW469714 LOC645744 similar to PCAF associated factor 65 beta isoform b 272801 242337_at 0186 AI347128 248179 217679_x_at 0240 AI683552 260844 230375_at 0303 AI936531 C6orf111 chromosome 6 open reading frame 111 271706 241242_at 0577 BE503118 272920 242456_at 0079 AA931565 MRE11A MRE11 meiotic recombination 11 homolog A (S. cerevisiae) 268417 237953_at 0171 AI092511 271732 241268_x_at 0306 AI939447 262856 232387_at 0359 AK025700 AP1GBP1 AP1 gamma subunit binding protein 1 248249 217749_at 0896 NM_016128 COPG coatomer protein complex, subunit gamma 269075 238611_at 0292 AI906424 273157 242693_at 0522 AW664859 246444 215936_s_at 0318 AK001657 KIAA1033 KIAA1033 274291 243827_at 0370 AL038125 237453 206792_x_at 0763 NM_000923 PDE4C phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila) 269728 239264_at 0529 AW973078 275230 244766_at 0676 BG180003 LOC440354 PI-3-kinase-related kinase SMG-1 pseudogene 253746 223254_s_at 0077 AA887053 KIAA1333 KIAA1333 274016 243552_at 0466 AW008914 273410 242946_at 0499 AW293276 CD53 CD53 molecule 260055 229586_at 0504 AW300405 CHD9 chromodomain helicase DNA binding protein 9 239076 208442_s_at 0754 NM_000051 ATM||LOC651610 ataxia telangiectasia mutated (includes complementation groups A, C and D) similar to Serine-protein kinase ATM (Ataxia telangiectasia mutated) (A-T, mutated) 275010 244546_at 0257 AI760495 CYCS cytochrome c, somatic 260997 230528_s_at 0228 AI651726 MGC2752 hypothetical protein MGC2752 273598 243134_at 0484 AW190862 CHD2 chromodomain helicase DNA binding protein 2 265990 235526_at 0595 BE748802 C11orf58 chromosome 11 open reading frame 58 256821 226350_at 0435 AU155565 CHML choroideremia-like (Rab escort protein 2) 240298 209675_s_at 0548 BC004242 HNRPUL1 heterogeneous nuclear ribonucleoprotein U-like 1 253682 223189_x_at 0476 AW082219 MLL5 myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila) 262364 231895_at 0024 AA501453 SASS6 spindle assembly 6 homolog (C. elegans) 273868 243404_at 0029 AA553477 255450 224977_at 0386 AL119182 C6orf89 chromosome 6 open reading frame 89 254234 223743_s_at 0539 BC000756 MRPL4 mitochondrial ribosomal protein L4 232220 201556_s_at 0546 BC002737 VAMP2 vesicle-associated membrane protein 2 (synaptobrevin 2) 255483 225010_at 0351 AK024913 CCDC6 coiled-coil domain containing 6 261662 231193_s_at 0571 BE326569 263781 233314_at 0326 AK021487 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 233906 203243_s_at 0861 NM_006457 PDLIM5 PDZ and LIM domain 5 268932 238468_at 0016 AA214704 TNRC6B trinucleotide repeat containing 6B 261248 230779_at 0649 BF594371 TNRC6B trinucleotide repeat containing 6B

TABLE 5 Fragment Id Name SEQ ID NO. Accession Symbol Gene Name 238391 207735_at 0913 NM_017831 RNF125 ring finger protein 125 239530 208900_s_at 0468 AW025108 TOP1 topoisomerase (DNA) I 243866 213350_at 0654 BF680255 RPS11 ribosomal protein S11 244919 214405_at 1014 Z39557 245632 215123_at 0375 AL049250 245771 215262_at 0115 AF052160 245901 215392_at 0428 AU148154 246029 215521_at 0335 AK023029 PHC3 polyhomeotic homolog 3 (Drosophila) 246107 215599_at 1012 X83300 GUSBP1 glucuronidase, beta pseudogene 1 LOC730390 similar to SMA4 SMA4 SMA4 247318 216813_at 0402 AL512728 247363 216858_x_at 0379 AL080112 247438 216933_x_at 0967 S67788 APC adenomatosis polyposis coli 252260 221765_at 0196 AI378044 UGCG UDP-glucose ceramide glucosyltransferase 252807 222313_at 0528 AW972359 252824 222330_at 0530 AW974995 254110 223619_x_at 0133 AF119841 PECR peroxisomal trans-2-enoyl-CoA reductase 255042 224568_x_at 0462 AW005982 MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non- coding RNA) 255711 225239_at 0188 AI355441 261578 231109_at 0962 R44974 261953 231484_at 0202 AI424825 262204 231735_s_at 0882 NM_014086 264429 233964_at 0381 AL110135 264725 234260_at 0390 AL122039 265453 234989_at 0445 AV699657 TncRNA trophoblast-derived noncoding RNA 266011 235547_at 0701 BG548427 267022 236558_at 0043 AA699809 268332 237868_x_at 0267 AI791828 268477 238013_at 0634 BF347859 268806 238342_at 0653 BF677084 269075 238611_at 0292 AI906424 271008 240544_at 0745 N23033 272288 241824_at 0002 AA019641 272333 241869_at 0469 AW026509 APOL6 apolipoprotein L, 6 273157 242693_at 0522 AW664859 274112 243648_at 0017 AA280627 ZC3H11A zinc finger CCCH-type containing 11A 274272 243808_at 0486 AW193531

TABLE 6 SEQ ID NO Accession No. 0001 AA012917.1 0002 AA019641.1 0003 AA029331.1 0004 AA031528.1 0005 AA045257.1 0006 AA058770.1 0007 AA126728.1 0008 AA126763.1 0009 AA131041.1 0010 AA133341.1 0011 AA142842.1 0012 AA149545.1 0013 AA156754.1 0014 AA194149.1 0015 AA203136.1 0016 AA214704.1 0017 AA280627.1 0018 AA359612.1 0019 AA416756.1 0020 AA436887.1 0021 AA455236.1 0022 AA468591.1 0023 AA489681.1 0024 AA501453.1 0025 AA521056.1 0026 AA521056.1 0027 AA530892.1 0028 AA530892.1 0030 AA580082.1 0031 AA601208.1 0032 AA602532.1 0033 AA603494.1 0034 AA632758.1 0035 AA633203.1 0036 AA635523.1 0037 AA642477.1 0038 AA650558.1 0039 AA664258.1 0040 AA664291.1 0041 AA679988.1 0042 AA699443.1 0043 AA699809.1 0044 AA702930.1 0045 AA703523.1 0046 AA715041.1 0047 AA721230.1 0048 AA732581.1 0049 AA732581.1 0050 AA741058.1 0051 AA742310.1 0052 AA743390.1 0053 AA744613.1 0054 AA744636.1 0055 AA744964.1 0056 AA748423.1 0057 AA749101.1 0058 AA758013.1 0059 AA780679.1 0060 AA789293.1 0061 AA806368.1 0062 AA806845.1 0063 AA811192.1 0064 AA811657.1 0065 AA814383.1 0066 AA825925.1 0067 AA827805.1 0068 AA827878.1 0069 AA828049.1 0070 AA829017.1 0071 AA843122.1 0072 AA868193.1 0073 AA872593.1 0074 AA873350.1 0075 AA876138.1 0076 AA877910.1 0077 AA887053.1 0078 AA916568.1 0079 AA931565.1 0080 AA993566.1 0081 AB002342.2 0084 AB011165.2 0085 AB014486.1 0086 AB014560.1 0087 AB019490.1 0088 AB023173.1 0090 AB033054.2 0091 AB035482.1 0092 AB043821.1 0093 AB044805.1 0094 AB051450.1 0095 AC003007.1 0096 AC003030.1 0097 AC004528.1 0098 AC004692.2 0099 AC004832.3 0102 AF000381.2 0103 AF000381.2 0104 AF001540.1 0106 AF010144.1 0107 AF021834.1 0108 AF022991.1 0109 AF037194.1 0110 AF041261.1 0111 AF041461.1 0112 AF044253.1 0113 AF044253.1 0114 AF047002.1 0116 AF056322.1 0117 AF063612.1 0118 AF064103.1 0119 AF065389.1 0121 AF070592.1 0122 AF070620.1 0123 AF078866.1 0124 AF086041.1 0126 AF092128.1 0129 AF112221.1 0130 AF113007.1 0131 AF113016.1 0132 AF116273.1 0133 AF119841.1 0134 AF132202.1 0135 AF132202.1 0136 AF141304.1 0137 AF143684.1 0138 AF159567.1 0139 AF165187.1 0140 AF172449.1 0141 AF176039.1 0142 AF194537.1 0143 AF194973.1 0144 AF212842.1 0146 AF222691.1 0147 AF241785.1 0148 AF255648.1 0149 AF268193.1 0150 AF274954.1 0151 AF302786.1 0152 AF307332.1 0153 AF315633.1 0154 AF317392.1 0155 AF326966.1 0156 AF327066.1 0157 AF339764.1 0159 AI026708.1 0161 AI041522.1 0162 AI052103.1 0163 AI057333.1 0164 AI064690.1 0165 AI073803.1 0166 AI075407.1 0167 AI078279.1 0168 AI083578.1 0169 AI084489.1 0170 AI092265.1 0171 AI092511.1 0172 AI123399.1 0173 AI129320.1 0174 AI139252.1 0175 AI148006.1 0176 AI241945.1 0177 AI248610.1 0178 AI249980.1 0179 AI263909.1 0181 AI283051.1 0182 AI332638.1 0183 AI336848.1 0184 AI337069.1 0185 AI341234.1 0186 AI347128.1 0187 AI348001.1 0188 AI355441.1 0190 AI361805.1 0191 AI363213.1 0192 AI369073.1 0193 AI373676.1 0194 AI377324.1 0195 AI378026.1 0196 AI378044.1 0197 AI379691.1 0198 AI380514.1 0199 AI393355.1 0200 AI418892.1 0201 AI420611.1 0202 AI424825.1 0203 AI434509.1 0204 AI440495.1 0205 AI445833.1 0206 AI458949.1 0207 AI459274.1 0208 AI472339.1 0209 AI472757.1 0210 AI473796.1 0211 AI475544.1 0212 AI492388.1 0213 AI510829.1 0214 AI523817.1 0215 AI561070.1 0216 AI569482.1 0217 AI571419.1 0218 AI571798.1 0219 AI590053.1 0220 AI590719.1 0221 AI625022.1 0222 AI632224.1 0223 AI632728.1 0225 AI633738.1 0228 AI651726.1 0229 AI652546.1 0230 AI652848.1 0231 AI652861.1 0232 AI652864.1 0233 AI655799.1 0234 AI673812.1 0235 AI674926.1 0236 AI678692.1 0238 AI681177.1 0239 AI681868.1 0240 AI683552.1 0241 AI683805.1 0242 AI684761.1 0243 AI688640.1 0244 AI689052.1 0245 AI697540.1 0246 AI732802.1 0247 AI733194.1 0248 AI738675.1 0249 AI738965.1 0250 AI741056.1 0251 AI742039.1 0252 AI742057.1 0253 AI742378.1 0254 AI742626.1 0255 AI753747.1 0256 AI754928.1 0257 AI760495.1 0259 AI761989.1 0260 AI762296.1 0261 AI762475.1 0262 AI763123.1 0263 AI763206.1 0264 AI767435.1 0265 AI767751.1 0266 AI768512.1 0267 AI791828.1 0268 AI796687.1 0269 AI797788.1 0270 AI805266.1 0271 AI806984.1 0272 AI807341.1 0274 AI809961.1 0275 AI810244.1 0276 AI814329.1 0277 AI814527.1 0278 AI818488.1 0279 AI819630.1 0281 AI820796.1 0282 AI821721.1 0284 AI827015.1 0285 AI828221.1 0286 AI829170.1 0287 AI829875.1 0288 AI832074.1 0289 AI857639.1 0290 AI860647.1 0291 AI871160.1 0292 AI906424.1 0293 AI914323.1 0295 AI923675.1 0296 AI924150.1 0297 AI924660.1 0298 AI925305.1 0299 AI925572.1 0300 AI927329.1 0301 AI927512.1 0302 AI934556.1 0303 AI936531.1 0304 AI937206.1 0305 AI939442.1 0306 AI939447.1 0307 AI950023.1 0308 AI963460.1 0309 AI970788.1 0310 AI979301.1 0311 AI982758.1 0312 AI983432.1 0313 AJ239383.1 0314 AJ275469.1 0315 AJ292969.1 0316 AK000667.1 0317 AK000677.1 0318 AK001657.1 0319 AK001728.1 0320 AK001731.1 0321 AK001734.1 0322 AK001816.1 0323 AK001822.1 0324 AK021431.1 0325 AK021457.1 0326 AK021487.1 0327 AK021525.1 0328 AK021569.1 0329 AK022100.1 0330 AK022166.1 0331 AK022188.1 0332 AK022280.1 0333 AK022303.1 0334 AK022473.1 0335 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1. A method for evaluating multiple sclerosis (MS) in a patient, comprising: determining a gene expression profile for a blood sample of a patient having or suspected of having MS, said gene expression profile comprising gene expression values for a plurality of genes that are differentially expressed in MS, said genes being listed in Tables 1-5; comparing said gene expression profile to an MS- and/or a non-MS profile; and classifying the gene expression profile as an MS profile or a non-MS profile.
 2. (canceled)
 3. The method of claim 1, wherein the gene expression profile is determined prior to treatment for MS.
 4. The method of claim 1, wherein said patient is being treated with at least one of Beta-interferon, Glatiramer acetate, and Natalizumab.
 5. The method of claim 1, wherein said patient is suspected of having MS.
 6. (canceled)
 7. (canceled)
 8. The method of claim 1, wherein the gene expression profile is determined after about 3 months of treatment, after about 6 months of treatment, and/or after about 12 months of treatment for MS.
 9. The method of claim 1, wherein classifying the gene expression profile as an MS profile or a non-MS profile includes determining a probability that the patient has MS.
 10. The method of claim 1, wherein the non-MS profile and/or the MS profile is matched to the patient by at least one of age, race, gender, and clinical manifestation of MS.
 11. The method of claim 1, wherein said MS profile is a relapsing—remitting MS profile.
 12. The method of claim 1, wherein the sample is a whole blood sample.
 13. The method of claim 11, wherein the genes that are differentially expressed in MS patients are listed in Table 1 or
 2. 14. The method of claim 1, wherein the sample is a white blood cell sample.
 15. The method of claim 14, wherein the genes that are differentially expressed in MS patients are listed in Table
 2. 16. (canceled)
 17. The method of claim 1, wherein said gene expression profile comprises the levels of expression for at least 7 genes listed in Table 1 or
 2. 18-21. (canceled)
 22. The method of claim 1, wherein said levels of expression have been normalized to the MS-profile and non-MS profile based on the level of expression of at least one constitutively expressed gene.
 23. The method of claim 1, wherein the sample is a Peripheral Blood Mononuclear Cell (PBMC) sample.
 24. The method of claim 1, wherein said gene expression profile is determined using a hybridization-based assay or a polymerase-based assay.
 25. The method of claim 1, wherein the gene expression profile is classified as an MS profile or a non-MS profile using one or more classification schemes selected from Naïve Bayes, Support Vector Machine, Nearest Neighbor, Decision Tree, Logistic, Artificial Neural Network, and Rule-based scheme.
 26. (canceled)
 27. A method for preparing a patient gene expression profile for evaluating MS, comprising, quantifying the level of expression of a plurality of genes listed in one or more of Tables 1-5 in a patient blood sample. 28-44. (canceled)
 45. A method for monitoring treatment of a multiple sclerosis patient, comprising: determining a pre-treatment gene expression profile and at least one post-treatment gene expression profile, said pre-treatment and said post-treatment gene expression profiles comprising gene expression values for a plurality of genes that are differentially expressed upon treatment for MS, said genes being listed in one of Tables 3-5; comparing said pre-treatment gene expression profile with said post-treatment gene expression profile; and identifying differences between the pre-treatment gene expression profile and the post-treatment gene expression profile, wherein said differences are indicative of effective treatment for MS. 46-54. (canceled)
 55. A computer system comprising a database on one or more computer readable medium, and containing mean gene expression values for at least ten genes in an MS patient population and in a non-MS patient population, said at least ten genes being selected from Table 1 and/or
 2. 56-65. (canceled)
 66. A kit for evaluating MS, comprising nucleic acid primers and/or probes for determining the level of expression in a patient sample of a plurality of genes listed in Tables 1-5.
 67. (canceled)
 68. (canceled) 